Starting phenix.real_space_refine on Tue Nov 18 01:08:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctw_45921/11_2025/9ctw_45921.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctw_45921/11_2025/9ctw_45921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ctw_45921/11_2025/9ctw_45921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctw_45921/11_2025/9ctw_45921.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctw_45921/11_2025/9ctw_45921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctw_45921/11_2025/9ctw_45921.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6226 2.51 5 N 1636 2.21 5 O 1848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9754 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1688 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Chain: "D" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1651 Classifications: {'peptide': 220} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Chain: "E" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1688 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Chain: "F" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1651 Classifications: {'peptide': 220} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Chain: "A" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1538 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1538 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Time building chain proxies: 2.69, per 1000 atoms: 0.28 Number of scatterers: 9754 At special positions: 0 Unit cell: (139.92, 92.432, 133.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1848 8.00 N 1636 7.00 C 6226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 202 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 202 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 415.2 milliseconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 19.4% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'C' and resid 83 through 87 removed outlier: 4.126A pdb=" N VAL C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.580A pdb=" N HIS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.883A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'E' and resid 83 through 87 removed outlier: 4.060A pdb=" N VAL E 87 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'E' and resid 187 through 193 removed outlier: 3.843A pdb=" N HIS E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.900A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.525A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 165 No H-bonds generated for 'chain 'F' and resid 163 through 165' Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.525A pdb=" N TRP A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 71 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 74 through 107 Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.745A pdb=" N PHE A 112 " --> pdb=" O MET A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 3.588A pdb=" N TRP B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 71 removed outlier: 3.969A pdb=" N TRP B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 74 through 107 Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.725A pdb=" N PHE B 112 " --> pdb=" O MET B 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.250A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.250A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.690A pdb=" N ASN C 141 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 137 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 158 removed outlier: 3.762A pdb=" N LYS C 153 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.553A pdb=" N GLU D 10 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 49 through 51 Processing sheet with id=AA9, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 131 removed outlier: 6.076A pdb=" N TYR D 182 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.133A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS E 111 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL E 13 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N MET E 37 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR E 53 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP E 39 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.133A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS E 111 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL E 13 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR E 101 " --> pdb=" O GLN E 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.673A pdb=" N ASN E 141 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL E 137 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR E 177 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 157 through 158 removed outlier: 3.779A pdb=" N LYS E 153 " --> pdb=" O THR E 197 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.495A pdb=" N GLU F 10 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA F 92 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 49 through 51 Processing sheet with id=AC2, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AC3, first strand: chain 'F' and resid 127 through 131 removed outlier: 6.024A pdb=" N TYR F 182 " --> pdb=" O GLY F 151 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AC5, first strand: chain 'A' and resid 127 through 133 removed outlier: 4.452A pdb=" N ILE A 118 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU A 167 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 200 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 180 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG A 198 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY A 182 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR A 196 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A 184 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 194 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG A 186 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY A 192 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 149 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 127 through 133 removed outlier: 4.448A pdb=" N ILE B 118 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU B 167 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 200 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS B 180 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG B 198 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY B 182 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR B 196 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER B 184 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 194 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 186 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY B 192 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B 149 " --> pdb=" O LEU B 156 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3077 1.34 - 1.46: 2453 1.46 - 1.58: 4410 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 10002 Sorted by residual: bond pdb=" CA TRP A 58 " pdb=" C TRP A 58 " ideal model delta sigma weight residual 1.521 1.533 -0.012 1.11e-02 8.12e+03 1.10e+00 bond pdb=" C ASP E 98 " pdb=" N PRO E 99 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 1.00e+00 bond pdb=" C LEU A 54 " pdb=" O LEU A 54 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.16e-02 7.43e+03 8.94e-01 bond pdb=" C ASP C 98 " pdb=" N PRO C 99 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.11e-01 bond pdb=" C ASN C 80 " pdb=" N PRO C 81 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.22e-01 ... (remaining 9997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 13234 1.28 - 2.57: 316 2.57 - 3.85: 58 3.85 - 5.13: 8 5.13 - 6.42: 4 Bond angle restraints: 13620 Sorted by residual: angle pdb=" CA PRO C 81 " pdb=" C PRO C 81 " pdb=" O PRO C 81 " ideal model delta sigma weight residual 123.07 119.37 3.70 1.38e+00 5.25e-01 7.20e+00 angle pdb=" C ARG E 54 " pdb=" N ALA E 55 " pdb=" CA ALA E 55 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.76e+00 angle pdb=" C ARG C 54 " pdb=" N ALA C 55 " pdb=" CA ALA C 55 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.75e+00 angle pdb=" C TYR B 204 " pdb=" N LYS B 205 " pdb=" CA LYS B 205 " ideal model delta sigma weight residual 121.54 125.22 -3.68 1.91e+00 2.74e-01 3.72e+00 angle pdb=" CA VAL D 190 " pdb=" C VAL D 190 " pdb=" N PRO D 191 " ideal model delta sigma weight residual 117.33 119.27 -1.94 1.01e+00 9.80e-01 3.68e+00 ... (remaining 13615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.53: 5415 12.53 - 25.07: 358 25.07 - 37.60: 96 37.60 - 50.13: 24 50.13 - 62.67: 9 Dihedral angle restraints: 5902 sinusoidal: 2266 harmonic: 3636 Sorted by residual: dihedral pdb=" CA MET D 34 " pdb=" C MET D 34 " pdb=" N ASN D 35 " pdb=" CA ASN D 35 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA MET F 34 " pdb=" C MET F 34 " pdb=" N ASN F 35 " pdb=" CA ASN F 35 " ideal model delta harmonic sigma weight residual -180.00 -162.74 -17.26 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASN F 35 " pdb=" C ASN F 35 " pdb=" N TRP F 36 " pdb=" CA TRP F 36 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 5899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 952 0.031 - 0.063: 373 0.063 - 0.094: 119 0.094 - 0.126: 73 0.126 - 0.157: 13 Chirality restraints: 1530 Sorted by residual: chirality pdb=" CA ILE C 52 " pdb=" N ILE C 52 " pdb=" C ILE C 52 " pdb=" CB ILE C 52 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA ILE E 52 " pdb=" N ILE E 52 " pdb=" C ILE E 52 " pdb=" CB ILE E 52 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1527 not shown) Planarity restraints: 1718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 155 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO F 156 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 156 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 156 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 155 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO D 156 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 122 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 123 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " 0.018 5.00e-02 4.00e+02 ... (remaining 1715 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2900 2.83 - 3.34: 7928 3.34 - 3.86: 15348 3.86 - 4.38: 17820 4.38 - 4.90: 32393 Nonbonded interactions: 76389 Sorted by model distance: nonbonded pdb=" OG1 THR C 186 " pdb=" OD1 ASP C 188 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR E 186 " pdb=" OD1 ASP E 188 " model vdw 2.330 3.040 nonbonded pdb=" NH1 ARG D 40 " pdb=" O GLU D 89 " model vdw 2.332 3.120 nonbonded pdb=" NH1 ARG F 40 " pdb=" O GLU F 89 " model vdw 2.335 3.120 nonbonded pdb=" O THR F 194 " pdb=" OG SER F 197 " model vdw 2.355 3.040 ... (remaining 76384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.350 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.003 0.029 10010 Z= 0.130 Angle : 0.512 6.416 13636 Z= 0.277 Chirality : 0.043 0.157 1530 Planarity : 0.004 0.046 1718 Dihedral : 9.735 62.666 3550 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.86 % Favored : 95.98 % Rotamer: Outliers : 0.74 % Allowed : 3.80 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.24), residues: 1244 helix: 1.13 (0.36), residues: 196 sheet: 0.35 (0.24), residues: 496 loop : -0.95 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.010 0.001 TYR E 53 PHE 0.018 0.002 PHE F 109 TRP 0.013 0.001 TRP F 33 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00290 (10002) covalent geometry : angle 0.51081 (13620) SS BOND : bond 0.00436 ( 8) SS BOND : angle 0.94702 ( 16) hydrogen bonds : bond 0.22371 ( 425) hydrogen bonds : angle 8.74436 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.389 Fit side-chains REVERT: C 107 LYS cc_start: 0.8653 (tttt) cc_final: 0.8090 (tptt) REVERT: C 174 ASP cc_start: 0.7479 (p0) cc_final: 0.6820 (t0) REVERT: E 107 LYS cc_start: 0.8633 (tttt) cc_final: 0.8126 (tptt) REVERT: E 174 ASP cc_start: 0.7429 (p0) cc_final: 0.6929 (t0) REVERT: F 103 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8676 (pm20) REVERT: A 107 ARG cc_start: 0.7152 (mtp180) cc_final: 0.6800 (mtp85) REVERT: A 135 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8287 (mt-10) REVERT: A 166 LYS cc_start: 0.8777 (mttt) cc_final: 0.8218 (mmtm) REVERT: B 135 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8216 (mt-10) REVERT: B 166 LYS cc_start: 0.8506 (mttt) cc_final: 0.7980 (mmtm) outliers start: 8 outliers final: 3 residues processed: 164 average time/residue: 0.1161 time to fit residues: 25.8834 Evaluate side-chains 108 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 157 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.166496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128514 restraints weight = 10734.888| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.01 r_work: 0.3184 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10010 Z= 0.147 Angle : 0.561 9.098 13636 Z= 0.296 Chirality : 0.045 0.153 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.119 54.333 1370 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.42 % Favored : 95.42 % Rotamer: Outliers : 1.30 % Allowed : 8.80 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.25), residues: 1244 helix: 1.77 (0.36), residues: 196 sheet: 0.49 (0.23), residues: 540 loop : -0.95 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 40 TYR 0.013 0.002 TYR E 53 PHE 0.019 0.002 PHE F 109 TRP 0.013 0.001 TRP F 33 HIS 0.004 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00348 (10002) covalent geometry : angle 0.55878 (13620) SS BOND : bond 0.00742 ( 8) SS BOND : angle 1.41682 ( 16) hydrogen bonds : bond 0.04808 ( 425) hydrogen bonds : angle 6.17120 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.424 Fit side-chains REVERT: C 107 LYS cc_start: 0.8497 (tttt) cc_final: 0.8014 (tptt) REVERT: C 174 ASP cc_start: 0.7487 (p0) cc_final: 0.7045 (t0) REVERT: E 107 LYS cc_start: 0.8519 (tttt) cc_final: 0.8030 (tptt) REVERT: E 174 ASP cc_start: 0.7433 (p0) cc_final: 0.6965 (t0) REVERT: F 142 MET cc_start: 0.5821 (mmm) cc_final: 0.5464 (mmm) REVERT: A 107 ARG cc_start: 0.6995 (mtp180) cc_final: 0.6569 (mtp85) REVERT: A 135 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8156 (mt-10) REVERT: A 166 LYS cc_start: 0.8716 (mttt) cc_final: 0.8210 (mmtm) REVERT: B 135 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 166 LYS cc_start: 0.8594 (mttt) cc_final: 0.8068 (mmtt) outliers start: 14 outliers final: 9 residues processed: 116 average time/residue: 0.0879 time to fit residues: 15.2245 Evaluate side-chains 102 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 81 optimal weight: 0.0030 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 105 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.4928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.167635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.125323 restraints weight = 10756.382| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.18 r_work: 0.3247 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10010 Z= 0.118 Angle : 0.514 8.956 13636 Z= 0.270 Chirality : 0.043 0.148 1530 Planarity : 0.004 0.044 1718 Dihedral : 4.943 52.811 1370 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.20 % Allowed : 10.74 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.25), residues: 1244 helix: 1.96 (0.36), residues: 196 sheet: 0.60 (0.24), residues: 544 loop : -0.88 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.011 0.001 TYR C 53 PHE 0.017 0.001 PHE D 109 TRP 0.011 0.001 TRP F 33 HIS 0.003 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00275 (10002) covalent geometry : angle 0.51271 (13620) SS BOND : bond 0.00656 ( 8) SS BOND : angle 1.06222 ( 16) hydrogen bonds : bond 0.04059 ( 425) hydrogen bonds : angle 5.47044 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.378 Fit side-chains REVERT: C 37 MET cc_start: 0.8255 (tpt) cc_final: 0.8005 (tpt) REVERT: C 107 LYS cc_start: 0.8532 (tttt) cc_final: 0.8033 (tptt) REVERT: C 174 ASP cc_start: 0.7326 (p0) cc_final: 0.6937 (t0) REVERT: E 107 LYS cc_start: 0.8523 (tttt) cc_final: 0.8013 (tptt) REVERT: E 174 ASP cc_start: 0.7362 (p0) cc_final: 0.6937 (t0) REVERT: F 142 MET cc_start: 0.5890 (mmm) cc_final: 0.5556 (mmm) REVERT: A 107 ARG cc_start: 0.6907 (mtp180) cc_final: 0.6528 (mtp85) REVERT: A 135 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8084 (mt-10) REVERT: A 166 LYS cc_start: 0.8683 (mttt) cc_final: 0.8219 (mmtm) REVERT: B 135 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 166 LYS cc_start: 0.8632 (mttt) cc_final: 0.8129 (mmtt) outliers start: 13 outliers final: 11 residues processed: 108 average time/residue: 0.0874 time to fit residues: 14.1997 Evaluate side-chains 109 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN D 39 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN F 39 GLN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.161270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121223 restraints weight = 10901.406| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.03 r_work: 0.3175 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 10010 Z= 0.288 Angle : 0.706 8.820 13636 Z= 0.365 Chirality : 0.050 0.178 1530 Planarity : 0.005 0.042 1718 Dihedral : 5.687 59.544 1370 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.39 % Favored : 94.45 % Rotamer: Outliers : 2.59 % Allowed : 10.56 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.24), residues: 1244 helix: 1.52 (0.35), residues: 196 sheet: 0.43 (0.23), residues: 540 loop : -1.14 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 150 TYR 0.012 0.002 TYR F 52 PHE 0.030 0.003 PHE F 109 TRP 0.017 0.002 TRP F 33 HIS 0.006 0.002 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00736 (10002) covalent geometry : angle 0.70228 (13620) SS BOND : bond 0.01059 ( 8) SS BOND : angle 2.14233 ( 16) hydrogen bonds : bond 0.05602 ( 425) hydrogen bonds : angle 5.76673 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.383 Fit side-chains REVERT: C 107 LYS cc_start: 0.8686 (tttt) cc_final: 0.8207 (tptt) REVERT: C 174 ASP cc_start: 0.7499 (p0) cc_final: 0.7106 (t0) REVERT: E 107 LYS cc_start: 0.8697 (tttt) cc_final: 0.8197 (tptt) REVERT: E 174 ASP cc_start: 0.7551 (p0) cc_final: 0.7111 (t0) REVERT: F 142 MET cc_start: 0.6033 (mmm) cc_final: 0.5656 (mmm) REVERT: A 107 ARG cc_start: 0.7103 (mtp180) cc_final: 0.6721 (mtp85) REVERT: A 135 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8197 (mt-10) REVERT: A 166 LYS cc_start: 0.8746 (mttt) cc_final: 0.8238 (mmtm) REVERT: B 135 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8177 (mt-10) REVERT: B 137 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7892 (mt-10) REVERT: B 166 LYS cc_start: 0.8615 (mttt) cc_final: 0.8148 (mmtm) outliers start: 28 outliers final: 22 residues processed: 124 average time/residue: 0.0983 time to fit residues: 17.3748 Evaluate side-chains 120 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 77 optimal weight: 0.0040 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 0.0470 chunk 63 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 overall best weight: 0.4290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.166037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126907 restraints weight = 10914.260| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.05 r_work: 0.3240 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10010 Z= 0.115 Angle : 0.518 8.333 13636 Z= 0.273 Chirality : 0.043 0.150 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.179 55.275 1370 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.18 % Favored : 95.66 % Rotamer: Outliers : 2.13 % Allowed : 12.04 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1244 helix: 1.91 (0.35), residues: 196 sheet: 0.64 (0.24), residues: 540 loop : -1.01 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 198 TYR 0.009 0.001 TYR C 53 PHE 0.016 0.001 PHE F 109 TRP 0.010 0.001 TRP F 33 HIS 0.004 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00265 (10002) covalent geometry : angle 0.51674 (13620) SS BOND : bond 0.00542 ( 8) SS BOND : angle 1.04953 ( 16) hydrogen bonds : bond 0.03969 ( 425) hydrogen bonds : angle 5.28099 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.441 Fit side-chains REVERT: C 107 LYS cc_start: 0.8664 (tttt) cc_final: 0.8120 (tptt) REVERT: C 174 ASP cc_start: 0.7441 (p0) cc_final: 0.6954 (t0) REVERT: E 107 LYS cc_start: 0.8678 (tttt) cc_final: 0.8150 (tptt) REVERT: E 174 ASP cc_start: 0.7457 (p0) cc_final: 0.6983 (t0) REVERT: F 142 MET cc_start: 0.6030 (mmm) cc_final: 0.5680 (mmm) REVERT: A 90 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6639 (mp) REVERT: A 107 ARG cc_start: 0.6988 (mtp180) cc_final: 0.6565 (mtp85) REVERT: A 135 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8135 (mt-10) REVERT: A 166 LYS cc_start: 0.8727 (mttt) cc_final: 0.8229 (mmtm) REVERT: B 90 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6684 (mp) REVERT: B 135 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 137 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7875 (mt-10) REVERT: B 166 LYS cc_start: 0.8697 (mttt) cc_final: 0.8164 (mmtt) outliers start: 23 outliers final: 17 residues processed: 112 average time/residue: 0.0802 time to fit residues: 13.5936 Evaluate side-chains 116 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 0.0570 overall best weight: 0.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.163597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121127 restraints weight = 10854.859| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.23 r_work: 0.3180 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10010 Z= 0.172 Angle : 0.580 8.777 13636 Z= 0.301 Chirality : 0.045 0.159 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.333 56.487 1370 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.74 % Favored : 95.10 % Rotamer: Outliers : 2.50 % Allowed : 12.04 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1244 helix: 1.84 (0.35), residues: 196 sheet: 0.60 (0.24), residues: 540 loop : -1.02 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 150 TYR 0.011 0.002 TYR C 53 PHE 0.022 0.002 PHE F 109 TRP 0.012 0.001 TRP D 33 HIS 0.005 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00428 (10002) covalent geometry : angle 0.57823 (13620) SS BOND : bond 0.00749 ( 8) SS BOND : angle 1.51604 ( 16) hydrogen bonds : bond 0.04468 ( 425) hydrogen bonds : angle 5.31760 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.320 Fit side-chains REVERT: C 107 LYS cc_start: 0.8596 (tttt) cc_final: 0.8078 (tptt) REVERT: C 174 ASP cc_start: 0.7338 (p0) cc_final: 0.6909 (t0) REVERT: D 112 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8086 (pt0) REVERT: E 107 LYS cc_start: 0.8620 (tttt) cc_final: 0.8107 (tptt) REVERT: E 174 ASP cc_start: 0.7345 (p0) cc_final: 0.6944 (t0) REVERT: F 142 MET cc_start: 0.6080 (mmm) cc_final: 0.5694 (mmt) REVERT: A 90 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6644 (mp) REVERT: A 107 ARG cc_start: 0.6958 (mtp180) cc_final: 0.6562 (mtp85) REVERT: A 135 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8113 (mt-10) REVERT: A 166 LYS cc_start: 0.8705 (mttt) cc_final: 0.8231 (mmtm) REVERT: B 90 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6612 (mp) REVERT: B 135 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8138 (mt-10) REVERT: B 137 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7903 (mt-10) REVERT: B 166 LYS cc_start: 0.8653 (mttt) cc_final: 0.8185 (mmtm) outliers start: 27 outliers final: 21 residues processed: 113 average time/residue: 0.0903 time to fit residues: 15.0062 Evaluate side-chains 122 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.164387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.119848 restraints weight = 10853.398| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.09 r_work: 0.3191 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10010 Z= 0.152 Angle : 0.558 8.800 13636 Z= 0.291 Chirality : 0.044 0.157 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.297 56.504 1370 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.58 % Favored : 95.26 % Rotamer: Outliers : 2.50 % Allowed : 12.50 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1244 helix: 1.90 (0.35), residues: 196 sheet: 0.59 (0.24), residues: 544 loop : -0.93 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 150 TYR 0.010 0.001 TYR E 53 PHE 0.021 0.002 PHE F 109 TRP 0.012 0.001 TRP F 33 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00376 (10002) covalent geometry : angle 0.55693 (13620) SS BOND : bond 0.00661 ( 8) SS BOND : angle 1.32357 ( 16) hydrogen bonds : bond 0.04230 ( 425) hydrogen bonds : angle 5.22092 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.306 Fit side-chains REVERT: C 107 LYS cc_start: 0.8573 (tttt) cc_final: 0.8053 (tptt) REVERT: C 174 ASP cc_start: 0.7382 (p0) cc_final: 0.6972 (t0) REVERT: D 112 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: E 107 LYS cc_start: 0.8585 (tttt) cc_final: 0.8076 (tptt) REVERT: E 174 ASP cc_start: 0.7337 (p0) cc_final: 0.6939 (t0) REVERT: F 142 MET cc_start: 0.6061 (mmm) cc_final: 0.5703 (mmt) REVERT: A 90 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6631 (mp) REVERT: A 107 ARG cc_start: 0.6906 (mtp180) cc_final: 0.6515 (mtp85) REVERT: A 135 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8086 (mt-10) REVERT: A 166 LYS cc_start: 0.8666 (mttt) cc_final: 0.8205 (mmtm) REVERT: B 90 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6570 (mp) REVERT: B 102 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7976 (tp) REVERT: B 135 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8139 (mt-10) REVERT: B 137 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 166 LYS cc_start: 0.8620 (mttt) cc_final: 0.8171 (mmtm) outliers start: 27 outliers final: 23 residues processed: 110 average time/residue: 0.0884 time to fit residues: 14.2814 Evaluate side-chains 118 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 18 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 83 optimal weight: 0.0170 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126940 restraints weight = 10839.461| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.03 r_work: 0.3142 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10010 Z= 0.143 Angle : 0.551 8.900 13636 Z= 0.286 Chirality : 0.044 0.154 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.244 57.205 1370 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.69 % Allowed : 12.50 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 1244 helix: 1.96 (0.35), residues: 196 sheet: 0.59 (0.24), residues: 544 loop : -0.90 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 101 TYR 0.010 0.001 TYR C 53 PHE 0.020 0.002 PHE F 109 TRP 0.012 0.001 TRP F 33 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00352 (10002) covalent geometry : angle 0.55007 (13620) SS BOND : bond 0.00649 ( 8) SS BOND : angle 1.22899 ( 16) hydrogen bonds : bond 0.04100 ( 425) hydrogen bonds : angle 5.16806 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.384 Fit side-chains REVERT: C 107 LYS cc_start: 0.8636 (tttt) cc_final: 0.8110 (tptt) REVERT: C 174 ASP cc_start: 0.7437 (p0) cc_final: 0.6984 (t0) REVERT: D 112 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8120 (pt0) REVERT: E 107 LYS cc_start: 0.8673 (tttt) cc_final: 0.8143 (tptt) REVERT: E 174 ASP cc_start: 0.7378 (p0) cc_final: 0.6932 (t0) REVERT: F 142 MET cc_start: 0.6057 (mmm) cc_final: 0.5662 (mmt) REVERT: A 90 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6607 (mp) REVERT: A 102 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7964 (tp) REVERT: A 107 ARG cc_start: 0.6961 (mtp180) cc_final: 0.6520 (mtp85) REVERT: A 135 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8134 (mt-10) REVERT: A 166 LYS cc_start: 0.8733 (mttt) cc_final: 0.8244 (mmtm) REVERT: B 90 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6557 (mp) REVERT: B 102 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7994 (tp) REVERT: B 135 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8176 (mt-10) REVERT: B 137 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8018 (mt-10) REVERT: B 166 LYS cc_start: 0.8689 (mttt) cc_final: 0.8202 (mmtm) outliers start: 29 outliers final: 22 residues processed: 112 average time/residue: 0.0926 time to fit residues: 15.2170 Evaluate side-chains 120 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 90 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.164499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.127424 restraints weight = 10782.423| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.84 r_work: 0.3146 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10010 Z= 0.148 Angle : 0.559 8.904 13636 Z= 0.289 Chirality : 0.044 0.155 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.257 57.969 1370 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.78 % Allowed : 12.41 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1244 helix: 1.97 (0.35), residues: 196 sheet: 0.60 (0.24), residues: 544 loop : -0.90 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 150 TYR 0.010 0.001 TYR C 53 PHE 0.020 0.002 PHE F 109 TRP 0.012 0.001 TRP D 33 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00364 (10002) covalent geometry : angle 0.55739 (13620) SS BOND : bond 0.00686 ( 8) SS BOND : angle 1.30860 ( 16) hydrogen bonds : bond 0.04114 ( 425) hydrogen bonds : angle 5.16085 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.428 Fit side-chains REVERT: C 107 LYS cc_start: 0.8648 (tttt) cc_final: 0.8120 (tptt) REVERT: C 174 ASP cc_start: 0.7438 (p0) cc_final: 0.7001 (t0) REVERT: D 112 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8112 (pt0) REVERT: E 107 LYS cc_start: 0.8671 (tttt) cc_final: 0.8145 (tptt) REVERT: E 174 ASP cc_start: 0.7340 (p0) cc_final: 0.6911 (t0) REVERT: F 142 MET cc_start: 0.6042 (mmm) cc_final: 0.5645 (mmt) REVERT: A 90 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6647 (mp) REVERT: A 102 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7962 (tp) REVERT: A 107 ARG cc_start: 0.6959 (mtp180) cc_final: 0.6518 (mtp85) REVERT: A 135 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8126 (mt-10) REVERT: A 166 LYS cc_start: 0.8748 (mttt) cc_final: 0.8249 (mmtm) REVERT: B 90 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6601 (mp) REVERT: B 102 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7993 (tp) REVERT: B 135 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8180 (mt-10) REVERT: B 137 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 166 LYS cc_start: 0.8692 (mttt) cc_final: 0.8199 (mmtm) outliers start: 30 outliers final: 24 residues processed: 114 average time/residue: 0.0908 time to fit residues: 15.3582 Evaluate side-chains 122 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 45 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 83 optimal weight: 0.0170 chunk 9 optimal weight: 0.3980 chunk 48 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 85 optimal weight: 0.0060 chunk 4 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 GLN B 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129496 restraints weight = 10701.158| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.94 r_work: 0.3229 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10010 Z= 0.101 Angle : 0.493 8.823 13636 Z= 0.257 Chirality : 0.042 0.144 1530 Planarity : 0.004 0.046 1718 Dihedral : 4.933 57.636 1370 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.67 % Allowed : 13.43 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1244 helix: 2.15 (0.35), residues: 196 sheet: 0.74 (0.24), residues: 544 loop : -0.82 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.009 0.001 TYR C 53 PHE 0.016 0.001 PHE F 109 TRP 0.010 0.001 TRP F 33 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00232 (10002) covalent geometry : angle 0.49201 (13620) SS BOND : bond 0.00519 ( 8) SS BOND : angle 0.84598 ( 16) hydrogen bonds : bond 0.03412 ( 425) hydrogen bonds : angle 4.88772 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.391 Fit side-chains REVERT: C 107 LYS cc_start: 0.8550 (tttt) cc_final: 0.8052 (tptt) REVERT: C 174 ASP cc_start: 0.7366 (p0) cc_final: 0.6950 (t0) REVERT: D 112 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8088 (pt0) REVERT: E 107 LYS cc_start: 0.8575 (tttt) cc_final: 0.8065 (tptt) REVERT: E 174 ASP cc_start: 0.7305 (p0) cc_final: 0.6905 (t0) REVERT: F 81 MET cc_start: 0.8864 (tmm) cc_final: 0.8630 (ttp) REVERT: F 142 MET cc_start: 0.6171 (mmm) cc_final: 0.5787 (mmt) REVERT: A 107 ARG cc_start: 0.6888 (mtp180) cc_final: 0.6483 (mtp85) REVERT: A 135 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 166 LYS cc_start: 0.8681 (mttt) cc_final: 0.8240 (mmtm) REVERT: B 135 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8103 (mt-10) REVERT: B 137 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7917 (mt-10) REVERT: B 166 LYS cc_start: 0.8616 (mttt) cc_final: 0.8192 (mmtm) outliers start: 18 outliers final: 17 residues processed: 110 average time/residue: 0.0873 time to fit residues: 14.4028 Evaluate side-chains 115 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 4 optimal weight: 0.0030 chunk 24 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 76 optimal weight: 0.0000 chunk 109 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 GLN B 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.167280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129813 restraints weight = 10795.408| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.08 r_work: 0.3191 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10010 Z= 0.100 Angle : 0.494 8.449 13636 Z= 0.257 Chirality : 0.042 0.143 1530 Planarity : 0.004 0.045 1718 Dihedral : 4.807 56.598 1370 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.85 % Allowed : 13.70 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1244 helix: 2.20 (0.35), residues: 196 sheet: 0.79 (0.24), residues: 544 loop : -0.75 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 101 TYR 0.010 0.001 TYR C 53 PHE 0.015 0.001 PHE F 109 TRP 0.010 0.001 TRP F 33 HIS 0.002 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00231 (10002) covalent geometry : angle 0.49301 (13620) SS BOND : bond 0.00507 ( 8) SS BOND : angle 0.86901 ( 16) hydrogen bonds : bond 0.03332 ( 425) hydrogen bonds : angle 4.78060 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.11 seconds wall clock time: 48 minutes 38.65 seconds (2918.65 seconds total)