Starting phenix.real_space_refine on Wed Jun 18 14:31:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6n_29775/06_2025/8g6n_29775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6n_29775/06_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_29775/06_2025/8g6n_29775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6n_29775/06_2025/8g6n_29775.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6n_29775/06_2025/8g6n_29775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6n_29775/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.01, per 1000 atoms: 0.56 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: 5.79 Conformation dependent library (CDL) restraints added in 1.7 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: 1.52 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: 7.61 Time building geometry restraints manager: 6.79 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: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.370 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 48.300 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.360 ------------------------------------------------------------------------------- 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 : 1.740 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: 0.5965 time to fit residues: 124.1987 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 : 2.193 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.078461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060742 restraints weight = 112121.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.063184 restraints weight = 46846.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064712 restraints weight = 28667.520| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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= 0.169 Angle : 0.535 8.425 14969 Z= 0.277 Chirality : 0.037 0.153 1678 Planarity : 0.005 0.063 1941 Dihedral : 3.983 23.345 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 4.07762 ( 2124) covalent geometry : bond 0.00369 (11015) covalent geometry : angle 0.53466 (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 : 1.845 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: 0.8455 (mtm) cc_final: 0.8049 (mtm) REVERT: E 144 MET cc_start: 0.8212 (tmm) cc_final: 0.7893 (tmm) REVERT: F 133 TRP cc_start: 0.8555 (m-10) cc_final: 0.8338 (m-10) REVERT: F 144 MET cc_start: 0.8315 (ttt) cc_final: 0.8099 (ttm) outliers start: 16 outliers final: 8 residues processed: 148 average time/residue: 0.5113 time to fit residues: 106.2379 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 : 1.728 ------------------------------------------------------------------------------- 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: 5.9990 chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 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: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.077849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.060056 restraints weight = 112475.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.062497 restraints weight = 46717.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.064042 restraints weight = 28529.908| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11015 Z= 0.167 Angle : 0.520 7.471 14969 Z= 0.269 Chirality : 0.037 0.146 1678 Planarity : 0.004 0.052 1941 Dihedral : 3.903 17.600 1462 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.64 % Allowed : 14.46 % 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: 1.99 (0.23), residues: 1351 helix: 1.91 (0.16), residues: 991 sheet: -3.84 (1.14), residues: 9 loop : -0.16 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 184 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 0.004 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 715) hydrogen bonds : angle 4.02892 ( 2124) covalent geometry : bond 0.00363 (11015) covalent geometry : angle 0.52045 (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 152 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.683 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: 0.7497 (OUTLIER) cc_final: 0.7222 (t-90) REVERT: C 214 MET cc_start: 0.8561 (mtm) cc_final: 0.8222 (mtm) REVERT: E 144 MET cc_start: 0.8219 (tmm) cc_final: 0.7830 (tmm) REVERT: E 210 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8364 (p) REVERT: F 133 TRP cc_start: 0.8577 (m-10) cc_final: 0.8242 (m-10) outliers start: 19 outliers final: 13 residues processed: 148 average time/residue: 0.5598 time to fit residues: 114.3377 Evaluate side-chains 146 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.077432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059595 restraints weight = 112868.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.062023 restraints weight = 46795.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063542 restraints weight = 28596.989| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1357 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= 0.174 Angle : 0.511 5.127 14969 Z= 0.267 Chirality : 0.036 0.144 1678 Planarity : 0.004 0.049 1941 Dihedral : 3.910 17.870 1462 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.72 % Allowed : 14.72 % 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: 1.95 (0.23), residues: 1351 helix: 1.88 (0.16), residues: 991 sheet: -3.85 (1.23), residues: 9 loop : -0.19 (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 A 84 PHE 0.009 0.001 PHE A 32 TYR 0.011 0.001 TYR D 169 ARG 0.005 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 715) hydrogen bonds : angle 4.05806 ( 2124) covalent geometry : bond 0.00377 (11015) covalent geometry : angle 0.51087 (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 154 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.742 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: 0.7550 (OUTLIER) cc_final: 0.7260 (t-90) REVERT: C 214 MET cc_start: 0.8579 (mtm) cc_final: 0.8241 (mtm) REVERT: E 144 MET cc_start: 0.8229 (tmm) cc_final: 0.7941 (tmm) REVERT: E 210 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8404 (p) REVERT: F 133 TRP cc_start: 0.8626 (m-10) cc_final: 0.8257 (m-10) outliers start: 20 outliers final: 17 residues processed: 148 average time/residue: 0.5704 time to fit residues: 117.0162 Evaluate side-chains 150 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 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: 2.9990 chunk 82 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.078057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.060269 restraints weight = 112264.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062724 restraints weight = 46130.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.064237 restraints weight = 28039.372| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11015 Z= 0.121 Angle : 0.478 4.747 14969 Z= 0.245 Chirality : 0.036 0.141 1678 Planarity : 0.004 0.050 1941 Dihedral : 3.782 15.635 1462 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.38 % Allowed : 15.15 % 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: 2.22 (0.23), residues: 1351 helix: 2.07 (0.16), residues: 992 sheet: -3.65 (1.21), residues: 9 loop : -0.07 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 80 HIS 0.002 0.001 HIS E 120 PHE 0.008 0.001 PHE A 32 TYR 0.011 0.001 TYR D 164 ARG 0.004 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 715) hydrogen bonds : angle 3.86749 ( 2124) covalent geometry : bond 0.00268 (11015) covalent geometry : angle 0.47834 (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 154 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.709 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: 0.7551 (OUTLIER) cc_final: 0.7263 (t-90) REVERT: B 96 MET cc_start: 0.4655 (ppp) cc_final: 0.4339 (ppp) REVERT: C 214 MET cc_start: 0.8593 (mtm) cc_final: 0.8295 (mtm) REVERT: E 28 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: F 133 TRP cc_start: 0.8630 (m-10) cc_final: 0.8243 (m-10) outliers start: 16 outliers final: 12 residues processed: 150 average time/residue: 0.5652 time to fit residues: 117.3401 Evaluate side-chains 148 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 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 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: 1.9990 chunk 88 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.078180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.060424 restraints weight = 111548.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062865 restraints weight = 46126.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.064398 restraints weight = 28111.882| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1492 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= 0.118 Angle : 0.476 4.574 14969 Z= 0.243 Chirality : 0.035 0.144 1678 Planarity : 0.004 0.052 1941 Dihedral : 3.688 14.174 1460 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.38 % Allowed : 15.49 % Favored : 83.13 % 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: 2.35 (0.23), residues: 1351 helix: 2.15 (0.16), residues: 991 sheet: -3.58 (1.22), residues: 9 loop : 0.04 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.002 0.001 HIS A 84 PHE 0.008 0.001 PHE A 32 TYR 0.012 0.001 TYR D 164 ARG 0.006 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 715) hydrogen bonds : angle 3.81573 ( 2124) covalent geometry : bond 0.00263 (11015) covalent geometry : angle 0.47614 (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 154 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 2.148 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: 0.7561 (OUTLIER) cc_final: 0.7273 (t-90) REVERT: B 96 MET cc_start: 0.4694 (ppp) cc_final: 0.4361 (ppp) REVERT: C 214 MET cc_start: 0.8606 (mtm) cc_final: 0.8321 (mtm) REVERT: E 28 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: F 133 TRP cc_start: 0.8603 (m-10) cc_final: 0.8208 (m-10) outliers start: 16 outliers final: 14 residues processed: 150 average time/residue: 0.5815 time to fit residues: 122.9842 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 : 1.835 ------------------------------------------------------------------------------- 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 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 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: 0.0980 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.078667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.060960 restraints weight = 111816.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.063439 restraints weight = 45643.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064969 restraints weight = 27636.894| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11015 Z= 0.096 Angle : 0.469 7.025 14969 Z= 0.235 Chirality : 0.035 0.140 1678 Planarity : 0.004 0.053 1941 Dihedral : 3.607 14.095 1460 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.29 % Allowed : 15.92 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 992 sheet: -3.47 (1.22), residues: 9 loop : 0.14 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.002 0.000 HIS E 120 PHE 0.006 0.001 PHE A 32 TYR 0.014 0.001 TYR E 145 ARG 0.007 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03274 ( 715) hydrogen bonds : angle 3.68827 ( 2124) covalent geometry : bond 0.00217 (11015) covalent geometry : angle 0.46869 (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 158 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 1.656 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: 0.7405 (OUTLIER) cc_final: 0.7134 (t-90) REVERT: B 96 MET cc_start: 0.4647 (ppp) cc_final: 0.4317 (ppp) REVERT: C 214 MET cc_start: 0.8601 (mtm) cc_final: 0.8278 (mtm) REVERT: E 28 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: F 133 TRP cc_start: 0.8579 (m-10) cc_final: 0.8119 (m-10) outliers start: 15 outliers final: 11 residues processed: 155 average time/residue: 0.5503 time to fit residues: 118.0242 Evaluate side-chains 149 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 58 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.078115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.060228 restraints weight = 113030.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062695 restraints weight = 46770.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.064228 restraints weight = 28477.665| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1597 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= 0.135 Angle : 0.488 5.154 14969 Z= 0.250 Chirality : 0.036 0.141 1678 Planarity : 0.004 0.057 1941 Dihedral : 3.627 13.995 1460 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.38 % Allowed : 16.09 % Favored : 82.53 % 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: 2.44 (0.23), residues: 1351 helix: 2.21 (0.16), residues: 992 sheet: -3.65 (1.26), residues: 9 loop : 0.07 (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 D 164 ARG 0.007 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 715) hydrogen bonds : angle 3.77962 ( 2124) covalent geometry : bond 0.00298 (11015) covalent geometry : angle 0.48819 (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 153 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.603 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: 0.7156 (t-90) REVERT: B 96 MET cc_start: 0.4563 (ppp) cc_final: 0.4226 (ppp) REVERT: B 185 MET cc_start: 0.7500 (mtp) cc_final: 0.7129 (mtp) REVERT: C 214 MET cc_start: 0.8603 (mtm) cc_final: 0.8300 (mtm) REVERT: E 28 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: E 185 MET cc_start: 0.8469 (mtt) cc_final: 0.8257 (mtp) REVERT: F 55 MET cc_start: 0.7956 (ttm) cc_final: 0.7717 (mtp) REVERT: F 133 TRP cc_start: 0.8597 (m-10) cc_final: 0.8145 (m-10) REVERT: F 143 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7754 (mmm160) outliers start: 16 outliers final: 13 residues processed: 150 average time/residue: 0.5620 time to fit residues: 116.5528 Evaluate side-chains 152 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 108 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.078556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060828 restraints weight = 112215.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.063304 restraints weight = 46068.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.064830 restraints weight = 27961.083| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11015 Z= 0.109 Angle : 0.478 4.995 14969 Z= 0.242 Chirality : 0.035 0.139 1678 Planarity : 0.004 0.058 1941 Dihedral : 3.577 14.114 1460 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.46 % Allowed : 16.18 % Favored : 82.36 % 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: -3.55 (1.27), residues: 9 loop : 0.16 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 184 HIS 0.004 0.000 HIS E 120 PHE 0.007 0.001 PHE G 40 TYR 0.012 0.001 TYR D 164 ARG 0.008 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 715) hydrogen bonds : angle 3.69359 ( 2124) covalent geometry : bond 0.00246 (11015) covalent geometry : angle 0.47769 (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 157 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.601 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: 0.7418 (OUTLIER) cc_final: 0.7143 (t-90) REVERT: G 162 ARG cc_start: 0.7166 (mmt180) cc_final: 0.6526 (mmp80) REVERT: B 96 MET cc_start: 0.4637 (ppp) cc_final: 0.4311 (ppp) REVERT: B 176 GLN cc_start: 0.8114 (mp10) cc_final: 0.7847 (mp10) REVERT: B 185 MET cc_start: 0.7499 (mtp) cc_final: 0.7143 (mtp) REVERT: C 214 MET cc_start: 0.8609 (mtm) cc_final: 0.8301 (mtm) REVERT: E 28 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: F 133 TRP cc_start: 0.8576 (m-10) cc_final: 0.8117 (m-10) REVERT: F 143 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7764 (mmm160) outliers start: 17 outliers final: 14 residues processed: 154 average time/residue: 0.5633 time to fit residues: 117.6020 Evaluate side-chains 155 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 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: 0.9980 chunk 130 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.078521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060757 restraints weight = 112998.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.063223 restraints weight = 46338.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064768 restraints weight = 28106.220| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11015 Z= 0.117 Angle : 0.486 6.376 14969 Z= 0.247 Chirality : 0.035 0.140 1678 Planarity : 0.004 0.061 1941 Dihedral : 3.571 14.080 1460 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.55 % Allowed : 16.09 % Favored : 82.36 % 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: 2.56 (0.23), residues: 1351 helix: 2.30 (0.16), residues: 991 sheet: -3.48 (1.29), residues: 9 loop : 0.14 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 D 164 ARG 0.008 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 715) hydrogen bonds : angle 3.72586 ( 2124) covalent geometry : bond 0.00262 (11015) covalent geometry : angle 0.48615 (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 158 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 HIS cc_start: 0.7426 (OUTLIER) cc_final: 0.7146 (t-90) REVERT: G 162 ARG cc_start: 0.7126 (mmt180) cc_final: 0.6490 (mmp80) REVERT: B 96 MET cc_start: 0.4650 (ppp) cc_final: 0.4323 (ppp) REVERT: B 185 MET cc_start: 0.7504 (mtp) cc_final: 0.7151 (mtp) REVERT: C 214 MET cc_start: 0.8622 (mtm) cc_final: 0.8290 (mtm) REVERT: E 28 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: F 133 TRP cc_start: 0.8576 (m-10) cc_final: 0.8122 (m-10) REVERT: F 143 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7762 (mmm160) outliers start: 18 outliers final: 15 residues processed: 154 average time/residue: 0.7114 time to fit residues: 151.4429 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 : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 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: 0.5980 chunk 23 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.078429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060547 restraints weight = 112423.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.063020 restraints weight = 46569.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.064561 restraints weight = 28371.122| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11015 Z= 0.127 Angle : 0.497 7.536 14969 Z= 0.252 Chirality : 0.036 0.144 1678 Planarity : 0.004 0.060 1941 Dihedral : 3.605 14.130 1460 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.46 % Allowed : 16.35 % Favored : 82.19 % 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: 2.52 (0.23), residues: 1351 helix: 2.26 (0.16), residues: 991 sheet: -3.46 (1.30), residues: 9 loop : 0.14 (0.34), residues: 351 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 0.03327 ( 715) hydrogen bonds : angle 3.77156 ( 2124) covalent geometry : bond 0.00283 (11015) covalent geometry : angle 0.49711 (14969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6763.75 seconds wall clock time: 117 minutes 36.97 seconds (7056.97 seconds total)