Starting phenix.real_space_refine on Sun Jul 27 22:03:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctw_45921/07_2025/9ctw_45921.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctw_45921/07_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_45921/07_2025/9ctw_45921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctw_45921/07_2025/9ctw_45921.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctw_45921/07_2025/9ctw_45921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctw_45921/07_2025/9ctw_45921.cif" } resolution = 3.01 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= 0.012 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.86, per 1000 atoms: 0.70 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.23 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: 2.89 Time building geometry restraints manager: 2.68 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: 0.02 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: 5.070 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.230 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.110 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.013 0.001 TRP F 33 HIS 0.002 0.001 HIS A 154 PHE 0.018 0.002 PHE F 109 TYR 0.010 0.001 TYR E 53 ARG 0.002 0.000 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.22371 ( 425) hydrogen bonds : angle 8.74436 ( 1128) SS BOND : bond 0.00436 ( 8) SS BOND : angle 0.94702 ( 16) covalent geometry : bond 0.00290 (10002) covalent geometry : angle 0.51081 (13620) *********************** 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 : 1.189 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: 0.2487 time to fit residues: 55.2830 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 : 0.989 ------------------------------------------------------------------------------- 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 104 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.165763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128321 restraints weight = 10706.830| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.82 r_work: 0.3178 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10010 Z= 0.168 Angle : 0.584 9.463 13636 Z= 0.308 Chirality : 0.045 0.157 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.200 54.824 1370 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.58 % Favored : 95.26 % Rotamer: Outliers : 1.39 % Allowed : 8.80 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.24), residues: 1244 helix: 1.70 (0.36), residues: 196 sheet: 0.58 (0.24), residues: 530 loop : -0.96 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 33 HIS 0.005 0.001 HIS C 202 PHE 0.022 0.002 PHE F 109 TYR 0.012 0.002 TYR E 53 ARG 0.003 0.000 ARG C 112 Details of bonding type rmsd hydrogen bonds : bond 0.05081 ( 425) hydrogen bonds : angle 6.25540 ( 1128) SS BOND : bond 0.00858 ( 8) SS BOND : angle 1.53659 ( 16) covalent geometry : bond 0.00407 (10002) covalent geometry : angle 0.58231 (13620) *********************** 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 117 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.252 Fit side-chains REVERT: C 107 LYS cc_start: 0.8560 (tttt) cc_final: 0.8037 (tptt) REVERT: C 174 ASP cc_start: 0.7484 (p0) cc_final: 0.7033 (t0) REVERT: E 107 LYS cc_start: 0.8561 (tttt) cc_final: 0.8043 (tptt) REVERT: E 174 ASP cc_start: 0.7420 (p0) cc_final: 0.6935 (t0) REVERT: F 142 MET cc_start: 0.5770 (mmm) cc_final: 0.5441 (mmm) REVERT: A 107 ARG cc_start: 0.7016 (mtp180) cc_final: 0.6641 (mtp85) REVERT: A 135 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8179 (mt-10) REVERT: A 166 LYS cc_start: 0.8721 (mttt) cc_final: 0.8207 (mmtm) REVERT: B 135 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8209 (mt-10) REVERT: B 166 LYS cc_start: 0.8627 (mttt) cc_final: 0.8085 (mmtt) outliers start: 15 outliers final: 10 residues processed: 114 average time/residue: 0.1910 time to fit residues: 32.7671 Evaluate side-chains 103 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 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 A residue 70 VAL Chi-restraints excluded: chain A residue 197 SER 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 27 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.164251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122739 restraints weight = 10869.880| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.14 r_work: 0.3215 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 : 0.004 0.044 10010 Z= 0.167 Angle : 0.580 9.133 13636 Z= 0.303 Chirality : 0.045 0.159 1530 Planarity : 0.004 0.044 1718 Dihedral : 5.292 55.766 1370 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.58 % Favored : 95.26 % Rotamer: Outliers : 1.76 % Allowed : 11.11 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.16 (0.24), residues: 1244 helix: 1.75 (0.35), residues: 196 sheet: 0.55 (0.24), residues: 540 loop : -1.04 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 33 HIS 0.004 0.001 HIS C 202 PHE 0.022 0.002 PHE F 109 TYR 0.011 0.002 TYR C 53 ARG 0.002 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04719 ( 425) hydrogen bonds : angle 5.66502 ( 1128) SS BOND : bond 0.00745 ( 8) SS BOND : angle 1.46486 ( 16) covalent geometry : bond 0.00413 (10002) covalent geometry : angle 0.57780 (13620) *********************** 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 115 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.051 Fit side-chains REVERT: C 107 LYS cc_start: 0.8585 (tttt) cc_final: 0.8060 (tptt) REVERT: C 174 ASP cc_start: 0.7380 (p0) cc_final: 0.6979 (t0) REVERT: E 107 LYS cc_start: 0.8542 (tttt) cc_final: 0.8010 (tptt) REVERT: E 174 ASP cc_start: 0.7360 (p0) cc_final: 0.6919 (t0) REVERT: F 142 MET cc_start: 0.5903 (mmm) cc_final: 0.5566 (mmm) REVERT: A 107 ARG cc_start: 0.6940 (mtp180) cc_final: 0.6553 (mtp85) REVERT: A 135 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8108 (mt-10) REVERT: A 166 LYS cc_start: 0.8688 (mttt) cc_final: 0.8203 (mmtm) REVERT: B 135 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8098 (mt-10) REVERT: B 137 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 166 LYS cc_start: 0.8653 (mttt) cc_final: 0.8129 (mmtt) outliers start: 19 outliers final: 15 residues processed: 110 average time/residue: 0.1805 time to fit residues: 30.0824 Evaluate side-chains 111 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 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 157 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 197 SER 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 87 optimal weight: 1.9990 chunk 80 optimal weight: 0.0000 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 0.0670 chunk 105 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN F 50 GLN A 155 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.166987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122734 restraints weight = 10680.217| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.07 r_work: 0.3265 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10010 Z= 0.110 Angle : 0.502 9.073 13636 Z= 0.264 Chirality : 0.043 0.148 1530 Planarity : 0.004 0.046 1718 Dihedral : 4.984 52.812 1370 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 1.85 % Allowed : 11.30 % 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 (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: 0.35 (0.25), residues: 1244 helix: 1.99 (0.35), residues: 196 sheet: 0.64 (0.24), residues: 544 loop : -0.91 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 33 HIS 0.003 0.001 HIS A 155 PHE 0.016 0.001 PHE D 109 TYR 0.010 0.001 TYR C 53 ARG 0.002 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 425) hydrogen bonds : angle 5.23566 ( 1128) SS BOND : bond 0.00539 ( 8) SS BOND : angle 0.98486 ( 16) covalent geometry : bond 0.00256 (10002) covalent geometry : angle 0.50147 (13620) *********************** 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 117 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.977 Fit side-chains REVERT: C 107 LYS cc_start: 0.8635 (tttt) cc_final: 0.8033 (tptt) REVERT: C 174 ASP cc_start: 0.7366 (p0) cc_final: 0.6854 (t0) REVERT: E 107 LYS cc_start: 0.8665 (tttt) cc_final: 0.8074 (tptt) REVERT: E 174 ASP cc_start: 0.7385 (p0) cc_final: 0.6877 (t0) REVERT: F 142 MET cc_start: 0.5941 (mmm) cc_final: 0.5600 (mmm) REVERT: A 90 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6535 (mp) REVERT: A 107 ARG cc_start: 0.6867 (mtp180) cc_final: 0.6403 (mtp85) REVERT: A 135 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8135 (mt-10) REVERT: A 166 LYS cc_start: 0.8756 (mttt) cc_final: 0.8194 (mmtm) REVERT: B 90 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6499 (mp) REVERT: B 135 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8174 (mt-10) REVERT: B 137 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7712 (mt-10) REVERT: B 166 LYS cc_start: 0.8695 (mttt) cc_final: 0.8107 (mmtt) outliers start: 20 outliers final: 14 residues processed: 112 average time/residue: 0.2291 time to fit residues: 38.7294 Evaluate side-chains 112 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 127 SER Chi-restraints excluded: chain D residue 157 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.165530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123393 restraints weight = 10795.368| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.12 r_work: 0.3225 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10010 Z= 0.137 Angle : 0.536 8.906 13636 Z= 0.279 Chirality : 0.044 0.153 1530 Planarity : 0.004 0.046 1718 Dihedral : 5.062 54.320 1370 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.04 % Allowed : 11.48 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.37 (0.25), residues: 1244 helix: 1.99 (0.35), residues: 196 sheet: 0.66 (0.24), residues: 544 loop : -0.91 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 33 HIS 0.004 0.001 HIS A 155 PHE 0.019 0.002 PHE F 109 TYR 0.011 0.001 TYR C 53 ARG 0.002 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 425) hydrogen bonds : angle 5.18779 ( 1128) SS BOND : bond 0.00654 ( 8) SS BOND : angle 1.22266 ( 16) covalent geometry : bond 0.00333 (10002) covalent geometry : angle 0.53445 (13620) *********************** 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 118 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.058 Fit side-chains REVERT: C 107 LYS cc_start: 0.8548 (tttt) cc_final: 0.8029 (tptt) REVERT: C 174 ASP cc_start: 0.7350 (p0) cc_final: 0.6950 (t0) REVERT: E 107 LYS cc_start: 0.8588 (tttt) cc_final: 0.8076 (tptt) REVERT: E 174 ASP cc_start: 0.7347 (p0) cc_final: 0.6920 (t0) REVERT: F 142 MET cc_start: 0.6054 (mmm) cc_final: 0.5723 (mmt) REVERT: A 90 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6762 (mp) REVERT: A 107 ARG cc_start: 0.6909 (mtp180) cc_final: 0.6501 (mtp85) REVERT: A 135 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8083 (mt-10) REVERT: A 166 LYS cc_start: 0.8669 (mttt) cc_final: 0.8220 (mmtm) REVERT: B 90 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6784 (mp) REVERT: B 135 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8121 (mt-10) REVERT: B 137 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 166 LYS cc_start: 0.8627 (mttt) cc_final: 0.8175 (mmtm) outliers start: 22 outliers final: 20 residues processed: 113 average time/residue: 0.1811 time to fit residues: 31.1095 Evaluate side-chains 117 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 184 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 103 GLU 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 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 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 89 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 E 42 GLN F 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.161926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121415 restraints weight = 10851.139| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.10 r_work: 0.3165 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10010 Z= 0.232 Angle : 0.651 8.469 13636 Z= 0.336 Chirality : 0.048 0.169 1530 Planarity : 0.005 0.045 1718 Dihedral : 5.564 58.114 1370 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.06 % Favored : 94.77 % Rotamer: Outliers : 3.15 % Allowed : 10.93 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.10 (0.24), residues: 1244 helix: 1.74 (0.35), residues: 196 sheet: 0.51 (0.23), residues: 542 loop : -1.09 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 33 HIS 0.007 0.002 HIS A 155 PHE 0.025 0.002 PHE D 109 TYR 0.011 0.002 TYR C 53 ARG 0.004 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.05055 ( 425) hydrogen bonds : angle 5.49818 ( 1128) SS BOND : bond 0.00929 ( 8) SS BOND : angle 1.80414 ( 16) covalent geometry : bond 0.00588 (10002) covalent geometry : angle 0.64820 (13620) *********************** 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 131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 1.000 Fit side-chains REVERT: C 107 LYS cc_start: 0.8618 (tttt) cc_final: 0.8093 (tptt) REVERT: C 174 ASP cc_start: 0.7398 (p0) cc_final: 0.7008 (t0) REVERT: D 112 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8070 (pt0) REVERT: E 107 LYS cc_start: 0.8640 (tttt) cc_final: 0.8138 (tptt) REVERT: E 174 ASP cc_start: 0.7385 (p0) cc_final: 0.7000 (t0) REVERT: F 142 MET cc_start: 0.6074 (mmm) cc_final: 0.5698 (mmt) REVERT: A 90 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6562 (mp) REVERT: A 107 ARG cc_start: 0.6994 (mtp180) cc_final: 0.6624 (mtp85) REVERT: A 135 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8105 (mt-10) REVERT: A 166 LYS cc_start: 0.8706 (mttt) cc_final: 0.8223 (mmtm) REVERT: B 90 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6591 (mp) REVERT: B 135 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8133 (mt-10) REVERT: B 137 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7934 (mt-10) REVERT: B 166 LYS cc_start: 0.8649 (mttt) cc_final: 0.8164 (mmtm) outliers start: 34 outliers final: 26 residues processed: 119 average time/residue: 0.2036 time to fit residues: 35.8310 Evaluate side-chains 126 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 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 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 A residue 137 GLU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.164672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124855 restraints weight = 10861.333| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.15 r_work: 0.3237 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1998 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= 0.133 Angle : 0.539 8.790 13636 Z= 0.281 Chirality : 0.044 0.153 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.252 56.821 1370 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 2.59 % Allowed : 12.22 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.31 (0.25), residues: 1244 helix: 1.96 (0.35), residues: 196 sheet: 0.64 (0.24), residues: 542 loop : -0.99 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 33 HIS 0.003 0.001 HIS A 155 PHE 0.019 0.001 PHE F 109 TYR 0.010 0.001 TYR C 53 ARG 0.002 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 425) hydrogen bonds : angle 5.19260 ( 1128) SS BOND : bond 0.00607 ( 8) SS BOND : angle 1.19054 ( 16) covalent geometry : bond 0.00322 (10002) covalent geometry : angle 0.53805 (13620) *********************** 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 127 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.993 Fit side-chains REVERT: C 107 LYS cc_start: 0.8531 (tttt) cc_final: 0.8036 (tptt) REVERT: C 174 ASP cc_start: 0.7400 (p0) cc_final: 0.7017 (t0) REVERT: E 107 LYS cc_start: 0.8584 (tttt) cc_final: 0.8067 (tptt) REVERT: E 174 ASP cc_start: 0.7391 (p0) cc_final: 0.7024 (t0) REVERT: F 142 MET cc_start: 0.6059 (mmm) cc_final: 0.5713 (mmt) REVERT: A 90 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6756 (mp) REVERT: A 107 ARG cc_start: 0.6898 (mtp180) cc_final: 0.6513 (mtp85) REVERT: A 135 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8079 (mt-10) REVERT: A 166 LYS cc_start: 0.8670 (mttt) cc_final: 0.8223 (mmtm) REVERT: B 90 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6639 (mp) REVERT: B 102 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7979 (tp) REVERT: B 135 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 137 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7894 (mt-10) REVERT: B 166 LYS cc_start: 0.8625 (mttt) cc_final: 0.8189 (mmtm) outliers start: 28 outliers final: 23 residues processed: 118 average time/residue: 0.2023 time to fit residues: 35.1565 Evaluate side-chains 125 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 201 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 103 GLU 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 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 90 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 83 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 100 optimal weight: 0.0010 chunk 108 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.164131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124770 restraints weight = 10898.721| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.14 r_work: 0.3216 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10010 Z= 0.152 Angle : 0.560 8.854 13636 Z= 0.290 Chirality : 0.044 0.155 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.274 57.152 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 : 2.96 % Allowed : 12.13 % 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 (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: 0.31 (0.25), residues: 1244 helix: 1.96 (0.35), residues: 196 sheet: 0.60 (0.24), residues: 546 loop : -0.93 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 33 HIS 0.004 0.001 HIS A 155 PHE 0.020 0.002 PHE F 109 TYR 0.010 0.001 TYR C 53 ARG 0.002 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 425) hydrogen bonds : angle 5.18691 ( 1128) SS BOND : bond 0.00689 ( 8) SS BOND : angle 1.32889 ( 16) covalent geometry : bond 0.00373 (10002) covalent geometry : angle 0.55861 (13620) *********************** 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 130 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.955 Fit side-chains REVERT: C 107 LYS cc_start: 0.8553 (tttt) cc_final: 0.8059 (tptt) REVERT: C 174 ASP cc_start: 0.7414 (p0) cc_final: 0.7020 (t0) REVERT: D 112 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8067 (pt0) REVERT: E 107 LYS cc_start: 0.8611 (tttt) cc_final: 0.8095 (tptt) REVERT: E 174 ASP cc_start: 0.7361 (p0) cc_final: 0.6982 (t0) REVERT: F 142 MET cc_start: 0.6092 (mmm) cc_final: 0.5724 (mmt) REVERT: A 90 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6659 (mp) REVERT: A 102 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7947 (tp) REVERT: A 107 ARG cc_start: 0.6920 (mtp180) cc_final: 0.6509 (mtp85) REVERT: A 135 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8087 (mt-10) REVERT: A 166 LYS cc_start: 0.8671 (mttt) cc_final: 0.8219 (mmtm) REVERT: B 90 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6633 (mp) REVERT: B 102 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7975 (tp) REVERT: B 135 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8121 (mt-10) REVERT: B 137 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7930 (mt-10) REVERT: B 166 LYS cc_start: 0.8630 (mttt) cc_final: 0.8176 (mmtm) outliers start: 32 outliers final: 25 residues processed: 117 average time/residue: 0.1896 time to fit residues: 32.6631 Evaluate side-chains 127 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 34 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 112 GLN 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 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 A residue 137 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.163266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125608 restraints weight = 10791.962| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.06 r_work: 0.3150 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10010 Z= 0.172 Angle : 0.585 8.945 13636 Z= 0.303 Chirality : 0.045 0.159 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.403 58.743 1370 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.74 % Favored : 95.10 % Rotamer: Outliers : 2.78 % Allowed : 12.31 % 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 (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: 0.27 (0.25), residues: 1244 helix: 1.91 (0.35), residues: 196 sheet: 0.62 (0.24), residues: 542 loop : -0.99 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 33 HIS 0.005 0.001 HIS A 155 PHE 0.022 0.002 PHE F 109 TYR 0.010 0.002 TYR C 53 ARG 0.002 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 425) hydrogen bonds : angle 5.23261 ( 1128) SS BOND : bond 0.00761 ( 8) SS BOND : angle 1.49732 ( 16) covalent geometry : bond 0.00428 (10002) covalent geometry : angle 0.58302 (13620) *********************** 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 125 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.975 Fit side-chains REVERT: C 107 LYS cc_start: 0.8588 (tttt) cc_final: 0.8085 (tptt) REVERT: C 174 ASP cc_start: 0.7421 (p0) cc_final: 0.7010 (t0) REVERT: D 112 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8090 (pt0) REVERT: E 107 LYS cc_start: 0.8606 (tttt) cc_final: 0.8106 (tptt) REVERT: E 174 ASP cc_start: 0.7339 (p0) cc_final: 0.6947 (t0) REVERT: F 142 MET cc_start: 0.6119 (mmm) cc_final: 0.5734 (mmt) REVERT: A 90 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6669 (mp) REVERT: A 102 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8002 (tp) REVERT: A 107 ARG cc_start: 0.6909 (mtp180) cc_final: 0.6499 (mtp85) REVERT: A 135 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8088 (mt-10) REVERT: A 166 LYS cc_start: 0.8687 (mttt) cc_final: 0.8221 (mmtm) REVERT: B 90 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6635 (mp) REVERT: B 102 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8005 (tp) REVERT: B 135 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8109 (mt-10) REVERT: B 137 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7977 (mt-10) REVERT: B 166 LYS cc_start: 0.8619 (mttt) cc_final: 0.8157 (mmtm) outliers start: 30 outliers final: 23 residues processed: 113 average time/residue: 0.1887 time to fit residues: 31.8514 Evaluate side-chains 121 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 103 GLU Chi-restraints excluded: chain D residue 112 GLN 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 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 90 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.164260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126703 restraints weight = 10829.023| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.05 r_work: 0.3156 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10010 Z= 0.143 Angle : 0.548 8.787 13636 Z= 0.285 Chirality : 0.044 0.154 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.279 60.133 1370 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.66 % Favored : 95.26 % Rotamer: Outliers : 2.87 % Allowed : 12.59 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.34 (0.25), residues: 1244 helix: 2.01 (0.35), residues: 196 sheet: 0.61 (0.24), residues: 546 loop : -0.92 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 33 HIS 0.004 0.001 HIS A 155 PHE 0.020 0.002 PHE F 109 TYR 0.009 0.001 TYR C 53 ARG 0.002 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 425) hydrogen bonds : angle 5.11989 ( 1128) SS BOND : bond 0.00662 ( 8) SS BOND : angle 1.26882 ( 16) covalent geometry : bond 0.00352 (10002) covalent geometry : angle 0.54656 (13620) ********************** 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 125 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.191 Fit side-chains REVERT: C 107 LYS cc_start: 0.8622 (tttt) cc_final: 0.8088 (tptt) REVERT: C 174 ASP cc_start: 0.7432 (p0) cc_final: 0.6989 (t0) REVERT: D 81 MET cc_start: 0.8901 (tmm) cc_final: 0.8629 (ttp) REVERT: D 112 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8121 (pt0) REVERT: E 107 LYS cc_start: 0.8665 (tttt) cc_final: 0.8106 (tptt) REVERT: E 174 ASP cc_start: 0.7407 (p0) cc_final: 0.6977 (t0) REVERT: F 81 MET cc_start: 0.8911 (tmm) cc_final: 0.8619 (ttp) REVERT: F 142 MET cc_start: 0.6160 (mmm) cc_final: 0.5732 (mmt) REVERT: A 90 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6548 (mp) REVERT: A 102 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7950 (tp) REVERT: A 107 ARG cc_start: 0.6902 (mtp180) cc_final: 0.6451 (mtp85) REVERT: A 135 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8123 (mt-10) REVERT: A 166 LYS cc_start: 0.8749 (mttt) cc_final: 0.8255 (mmtm) REVERT: B 90 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6551 (mp) REVERT: B 102 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7974 (tp) REVERT: B 135 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8163 (mt-10) REVERT: B 137 GLU cc_start: 0.8235 (mt-10) cc_final: 0.8009 (mt-10) REVERT: B 166 LYS cc_start: 0.8673 (mttt) cc_final: 0.8181 (mmtm) outliers start: 31 outliers final: 24 residues processed: 112 average time/residue: 0.2607 time to fit residues: 43.6381 Evaluate side-chains 123 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 1.862 ------------------------------------------------------------------------------- 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 103 GLU Chi-restraints excluded: chain D residue 112 GLN 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 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 90 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 197 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 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 = 0.3912 r_free = 0.3912 target = 0.163881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126361 restraints weight = 10780.289| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.26 r_work: 0.3194 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10010 Z= 0.149 Angle : 0.556 8.731 13636 Z= 0.289 Chirality : 0.044 0.154 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.306 61.463 1370 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.66 % Favored : 95.26 % Rotamer: Outliers : 2.69 % Allowed : 12.69 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % 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: 0.33 (0.25), residues: 1244 helix: 2.00 (0.35), residues: 196 sheet: 0.61 (0.24), residues: 546 loop : -0.93 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 33 HIS 0.004 0.001 HIS A 155 PHE 0.020 0.002 PHE F 109 TYR 0.010 0.001 TYR C 53 ARG 0.002 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 425) hydrogen bonds : angle 5.10703 ( 1128) SS BOND : bond 0.00694 ( 8) SS BOND : angle 1.33758 ( 16) covalent geometry : bond 0.00366 (10002) covalent geometry : angle 0.55485 (13620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6018.46 seconds wall clock time: 106 minutes 29.59 seconds (6389.59 seconds total)