Starting phenix.real_space_refine on Wed May 21 10:57:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6n_29775/05_2025/8g6n_29775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6n_29775/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g6n_29775/05_2025/8g6n_29775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6n_29775/05_2025/8g6n_29775.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6n_29775/05_2025/8g6n_29775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6n_29775/05_2025/8g6n_29775.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 2, 'ARG:plan': 1} 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, 'GLU:plan': 1, 'ARG: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: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 10.16, per 1000 atoms: 0.47 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: 5.27 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.41 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: 6.68 Time building geometry restraints manager: 6.38 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: 2.100 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: 0.340 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.230 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.120 ------------------------------------------------------------------------------- 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 : 4.48 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), 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 TRP 0.029 0.001 TRP G 184 HIS 0.005 0.001 HIS E 120 PHE 0.035 0.002 PHE B 168 TYR 0.022 0.002 TYR E 145 ARG 0.017 0.001 ARG B 132 Details of bonding type rmsd hydrogen bonds : bond 0.09327 ( 715) hydrogen bonds : angle 4.32482 ( 2124) covalent geometry : bond 0.00417 (11015) covalent geometry : angle 0.73939 (14969) *********************** 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 : 1.920 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: 0.5912 time to fit residues: 122.8795 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 : 1.690 ------------------------------------------------------------------------------- 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 112 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 67 GLN F 193 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.078486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060720 restraints weight = 112115.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.063190 restraints weight = 46330.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064732 restraints weight = 28176.695| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11015 Z= 0.170 Angle : 0.535 8.426 14969 Z= 0.277 Chirality : 0.037 0.153 1678 Planarity : 0.005 0.063 1941 Dihedral : 3.983 23.343 1463 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.38 % Allowed : 14.63 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.23), residues: 1351 helix: 1.89 (0.16), residues: 990 sheet: -3.47 (1.10), residues: 9 loop : -0.08 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 184 HIS 0.004 0.001 HIS B 120 PHE 0.007 0.001 PHE A 32 TYR 0.010 0.001 TYR D 169 ARG 0.005 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 715) hydrogen bonds : angle 4.07761 ( 2124) covalent geometry : bond 0.00370 (11015) covalent geometry : angle 0.53471 (14969) *********************** 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 151 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.638 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: C 214 MET cc_start: 0.8506 (mtm) cc_final: 0.8104 (mtm) REVERT: E 144 MET cc_start: 0.8233 (tmm) cc_final: 0.7907 (tmm) REVERT: F 133 TRP cc_start: 0.8566 (m-10) cc_final: 0.8347 (m-10) REVERT: F 144 MET cc_start: 0.8327 (ttt) cc_final: 0.8110 (ttm) outliers start: 16 outliers final: 8 residues processed: 148 average time/residue: 0.5079 time to fit residues: 105.1816 Evaluate side-chains 137 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 D residue 197 ASP Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 214 MET 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 121 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS C 139 ASN C 176 GLN E 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.078176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.060426 restraints weight = 112452.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.062891 restraints weight = 46525.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.064429 restraints weight = 28296.447| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11015 Z= 0.150 Angle : 0.508 6.917 14969 Z= 0.261 Chirality : 0.036 0.147 1678 Planarity : 0.004 0.054 1941 Dihedral : 3.854 16.756 1462 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.29 % Allowed : 14.80 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.23), residues: 1351 helix: 1.98 (0.16), residues: 987 sheet: -3.80 (1.11), residues: 9 loop : -0.10 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 80 HIS 0.003 0.001 HIS E 120 PHE 0.008 0.001 PHE A 32 TYR 0.010 0.001 TYR D 169 ARG 0.003 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 715) hydrogen bonds : angle 3.96676 ( 2124) covalent geometry : bond 0.00327 (11015) covalent geometry : angle 0.50763 (14969) *********************** 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 151 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.895 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: C 214 MET cc_start: 0.8691 (mtm) cc_final: 0.8325 (mtm) REVERT: E 144 MET cc_start: 0.8216 (tmm) cc_final: 0.7830 (tmm) REVERT: F 133 TRP cc_start: 0.8565 (m-10) cc_final: 0.8234 (m-10) outliers start: 15 outliers final: 13 residues processed: 147 average time/residue: 0.5489 time to fit residues: 111.0344 Evaluate side-chains 146 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 152 ASP Chi-restraints excluded: chain D residue 45 GLU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.078124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.060248 restraints weight = 112682.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062709 restraints weight = 46634.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064246 restraints weight = 28455.481| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11015 Z= 0.135 Angle : 0.485 4.853 14969 Z= 0.249 Chirality : 0.036 0.141 1678 Planarity : 0.004 0.049 1941 Dihedral : 3.753 14.242 1460 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.55 % Allowed : 14.54 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.23), residues: 1351 helix: 2.07 (0.16), residues: 991 sheet: -3.75 (1.13), residues: 9 loop : -0.08 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 80 HIS 0.004 0.001 HIS E 120 PHE 0.009 0.001 PHE B 168 TYR 0.010 0.001 TYR D 169 ARG 0.004 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 715) hydrogen bonds : angle 3.89057 ( 2124) covalent geometry : bond 0.00296 (11015) covalent geometry : angle 0.48462 (14969) *********************** 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 156 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.615 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: 0.7514 (OUTLIER) cc_final: 0.7239 (t-90) REVERT: B 96 MET cc_start: 0.4695 (ppp) cc_final: 0.4397 (ppp) REVERT: C 214 MET cc_start: 0.8705 (mtm) cc_final: 0.8353 (mtm) REVERT: E 28 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: E 144 MET cc_start: 0.8221 (tmm) cc_final: 0.7940 (tmm) REVERT: E 210 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8284 (p) REVERT: F 133 TRP cc_start: 0.8600 (m-10) cc_final: 0.8240 (m-10) outliers start: 18 outliers final: 13 residues processed: 152 average time/residue: 0.5437 time to fit residues: 113.5996 Evaluate side-chains 150 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 48 THR 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 210 THR Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain F residue 41 SER 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 100 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.077756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059975 restraints weight = 112736.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.062428 restraints weight = 46574.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063942 restraints weight = 28286.656| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11015 Z= 0.153 Angle : 0.494 5.051 14969 Z= 0.257 Chirality : 0.036 0.142 1678 Planarity : 0.004 0.053 1941 Dihedral : 3.771 13.888 1460 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.81 % Allowed : 14.72 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.23), residues: 1351 helix: 2.02 (0.16), residues: 991 sheet: -3.70 (1.23), residues: 9 loop : -0.07 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 184 HIS 0.004 0.001 HIS A 84 PHE 0.008 0.001 PHE A 32 TYR 0.012 0.001 TYR D 164 ARG 0.005 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 715) hydrogen bonds : angle 3.94587 ( 2124) covalent geometry : bond 0.00336 (11015) covalent geometry : angle 0.49405 (14969) *********************** 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 155 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.930 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: 0.7548 (OUTLIER) cc_final: 0.7262 (t-90) REVERT: B 96 MET cc_start: 0.4748 (ppp) cc_final: 0.4429 (ppp) REVERT: C 214 MET cc_start: 0.8589 (mtm) cc_final: 0.8297 (mtm) REVERT: E 28 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: E 210 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8333 (p) REVERT: F 133 TRP cc_start: 0.8598 (m-10) cc_final: 0.8225 (m-10) outliers start: 21 outliers final: 17 residues processed: 149 average time/residue: 0.5424 time to fit residues: 112.0503 Evaluate side-chains 153 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 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 E residue 214 MET Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 96 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.078322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.060576 restraints weight = 111440.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.063025 restraints weight = 45927.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.064537 restraints weight = 27970.039| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11015 Z= 0.111 Angle : 0.470 4.924 14969 Z= 0.239 Chirality : 0.035 0.143 1678 Planarity : 0.004 0.049 1941 Dihedral : 3.666 14.060 1460 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.46 % Allowed : 14.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.23), residues: 1351 helix: 2.20 (0.16), residues: 992 sheet: -3.57 (1.22), residues: 9 loop : 0.04 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.003 0.001 HIS E 120 PHE 0.008 0.001 PHE A 32 TYR 0.011 0.001 TYR D 164 ARG 0.007 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 715) hydrogen bonds : angle 3.77917 ( 2124) covalent geometry : bond 0.00248 (11015) covalent geometry : angle 0.46957 (14969) *********************** 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 159 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.688 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: 0.7417 (OUTLIER) cc_final: 0.7141 (t-90) REVERT: B 96 MET cc_start: 0.4681 (ppp) cc_final: 0.4351 (ppp) REVERT: C 214 MET cc_start: 0.8607 (mtm) cc_final: 0.8300 (mtm) REVERT: E 28 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: E 210 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8294 (p) REVERT: F 133 TRP cc_start: 0.8579 (m-10) cc_final: 0.8130 (m-10) outliers start: 17 outliers final: 12 residues processed: 155 average time/residue: 0.5455 time to fit residues: 116.8126 Evaluate side-chains 153 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 215 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU 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 Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 58 optimal weight: 0.0270 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.078197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060391 restraints weight = 112297.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062842 restraints weight = 46206.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.064368 restraints weight = 28156.142| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11015 Z= 0.121 Angle : 0.484 6.953 14969 Z= 0.246 Chirality : 0.035 0.141 1678 Planarity : 0.004 0.055 1941 Dihedral : 3.653 14.027 1460 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.46 % Allowed : 15.92 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.23), residues: 1351 helix: 2.19 (0.16), residues: 992 sheet: -3.51 (1.27), residues: 9 loop : 0.04 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.004 0.001 HIS E 120 PHE 0.008 0.001 PHE A 32 TYR 0.012 0.001 TYR E 145 ARG 0.006 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 715) hydrogen bonds : angle 3.78211 ( 2124) covalent geometry : bond 0.00269 (11015) covalent geometry : angle 0.48366 (14969) *********************** 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: 17 poor density : 139 time to evaluate : 1.730 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: 0.7433 (OUTLIER) cc_final: 0.7164 (t-90) REVERT: B 96 MET cc_start: 0.4690 (ppp) cc_final: 0.4352 (ppp) REVERT: C 214 MET cc_start: 0.8605 (mtm) cc_final: 0.8283 (mtm) REVERT: E 28 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: E 210 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8300 (p) REVERT: F 133 TRP cc_start: 0.8581 (m-10) cc_final: 0.8134 (m-10) outliers start: 17 outliers final: 14 residues processed: 153 average time/residue: 0.5363 time to fit residues: 114.1332 Evaluate side-chains 153 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 58 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 95 optimal weight: 0.0470 chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.7284 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.078680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060871 restraints weight = 112706.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.063356 restraints weight = 46254.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.064895 restraints weight = 28101.868| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11015 Z= 0.101 Angle : 0.473 5.600 14969 Z= 0.238 Chirality : 0.035 0.139 1678 Planarity : 0.004 0.055 1941 Dihedral : 3.580 14.003 1460 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.64 % Allowed : 15.66 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.23), residues: 1351 helix: 2.30 (0.16), residues: 992 sheet: -3.42 (1.27), residues: 9 loop : 0.14 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.003 0.001 HIS E 120 PHE 0.007 0.001 PHE A 32 TYR 0.013 0.001 TYR D 164 ARG 0.008 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 715) hydrogen bonds : angle 3.69339 ( 2124) covalent geometry : bond 0.00229 (11015) covalent geometry : angle 0.47350 (14969) *********************** 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 158 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.974 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: 0.7417 (OUTLIER) cc_final: 0.7145 (t-90) REVERT: B 96 MET cc_start: 0.4686 (ppp) cc_final: 0.4353 (ppp) REVERT: B 185 MET cc_start: 0.7479 (mtp) cc_final: 0.7110 (mtp) REVERT: C 214 MET cc_start: 0.8600 (mtm) cc_final: 0.8279 (mtm) REVERT: E 28 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: F 133 TRP cc_start: 0.8562 (m-10) cc_final: 0.8113 (m-10) outliers start: 19 outliers final: 14 residues processed: 155 average time/residue: 0.5510 time to fit residues: 118.4462 Evaluate side-chains 153 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 63 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 105 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.078642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060829 restraints weight = 112218.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.063305 restraints weight = 46279.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.064842 restraints weight = 28219.397| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11015 Z= 0.112 Angle : 0.480 5.271 14969 Z= 0.243 Chirality : 0.035 0.140 1678 Planarity : 0.004 0.058 1941 Dihedral : 3.563 13.913 1460 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.46 % Allowed : 15.83 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.23), residues: 1351 helix: 2.31 (0.16), residues: 992 sheet: -3.57 (1.29), residues: 9 loop : 0.13 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 184 HIS 0.005 0.001 HIS E 120 PHE 0.007 0.001 PHE A 32 TYR 0.014 0.001 TYR E 145 ARG 0.008 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 715) hydrogen bonds : angle 3.70434 ( 2124) covalent geometry : bond 0.00252 (11015) covalent geometry : angle 0.48040 (14969) *********************** 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 155 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.773 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: 0.7430 (OUTLIER) cc_final: 0.7157 (t-90) REVERT: B 96 MET cc_start: 0.4729 (ppp) cc_final: 0.4402 (ppp) REVERT: B 185 MET cc_start: 0.7513 (mtp) cc_final: 0.7156 (mtp) REVERT: C 214 MET cc_start: 0.8600 (mtm) cc_final: 0.8272 (mtm) REVERT: E 28 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: E 185 MET cc_start: 0.8440 (mtt) cc_final: 0.8229 (mtp) REVERT: F 133 TRP cc_start: 0.8572 (m-10) cc_final: 0.8126 (m-10) outliers start: 17 outliers final: 14 residues processed: 152 average time/residue: 0.5369 time to fit residues: 113.1413 Evaluate side-chains 152 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 115 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 70 optimal weight: 0.0980 chunk 101 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.077937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.060041 restraints weight = 113204.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.062487 restraints weight = 47055.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.064016 restraints weight = 28701.012| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1675 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= 0.165 Angle : 0.513 6.078 14969 Z= 0.264 Chirality : 0.036 0.144 1678 Planarity : 0.004 0.061 1941 Dihedral : 3.663 14.064 1460 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.46 % Allowed : 16.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.23), residues: 1351 helix: 2.16 (0.16), residues: 992 sheet: -3.58 (1.31), residues: 9 loop : 0.04 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 184 HIS 0.004 0.001 HIS E 120 PHE 0.008 0.001 PHE A 32 TYR 0.013 0.001 TYR D 164 ARG 0.008 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 715) hydrogen bonds : angle 3.88131 ( 2124) covalent geometry : bond 0.00360 (11015) covalent geometry : angle 0.51260 (14969) ********************** 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 151 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 2.529 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: 0.7490 (OUTLIER) cc_final: 0.7208 (t-90) REVERT: B 96 MET cc_start: 0.4669 (ppp) cc_final: 0.4334 (ppp) REVERT: B 185 MET cc_start: 0.7540 (mtp) cc_final: 0.7177 (mtp) REVERT: C 214 MET cc_start: 0.8630 (mtm) cc_final: 0.8297 (mtm) REVERT: E 28 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: E 185 MET cc_start: 0.8461 (mtt) cc_final: 0.8254 (mtp) REVERT: F 133 TRP cc_start: 0.8607 (m-10) cc_final: 0.8175 (m-10) outliers start: 17 outliers final: 14 residues processed: 148 average time/residue: 0.5875 time to fit residues: 121.6602 Evaluate side-chains 148 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 96 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.078601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060750 restraints weight = 112241.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.063220 restraints weight = 46274.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064753 restraints weight = 28189.816| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1700 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= 0.108 Angle : 0.491 6.338 14969 Z= 0.248 Chirality : 0.035 0.142 1678 Planarity : 0.004 0.044 1941 Dihedral : 3.597 14.223 1460 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.46 % Allowed : 16.27 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.23), residues: 1351 helix: 2.28 (0.16), residues: 991 sheet: -3.49 (1.27), residues: 9 loop : 0.13 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 184 HIS 0.004 0.001 HIS E 120 PHE 0.007 0.001 PHE A 32 TYR 0.014 0.001 TYR E 145 ARG 0.002 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 715) hydrogen bonds : angle 3.74199 ( 2124) covalent geometry : bond 0.00244 (11015) covalent geometry : angle 0.49051 (14969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6384.23 seconds wall clock time: 111 minutes 32.28 seconds (6692.28 seconds total)