Starting phenix.real_space_refine on Tue May 13 05:28:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctw_45921/05_2025/9ctw_45921.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctw_45921/05_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_45921/05_2025/9ctw_45921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctw_45921/05_2025/9ctw_45921.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctw_45921/05_2025/9ctw_45921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctw_45921/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.82, 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: 2.51 Conformation dependent library (CDL) restraints added in 1.3 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: 1.47 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: 2.87 Time building geometry restraints manager: 2.93 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: 4.750 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: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.970 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.460 ------------------------------------------------------------------------------- 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 : 1.028 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: 0.2432 time to fit residues: 53.9508 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 : 0.991 ------------------------------------------------------------------------------- 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 = 10706.831| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.82 r_work: 0.3177 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 1.056 Fit side-chains REVERT: C 107 LYS cc_start: 0.8574 (tttt) cc_final: 0.8045 (tptt) REVERT: C 174 ASP cc_start: 0.7489 (p0) cc_final: 0.7041 (t0) REVERT: E 107 LYS cc_start: 0.8573 (tttt) cc_final: 0.8051 (tptt) REVERT: E 174 ASP cc_start: 0.7430 (p0) cc_final: 0.6949 (t0) REVERT: F 142 MET cc_start: 0.5759 (mmm) cc_final: 0.5426 (mmm) REVERT: A 107 ARG cc_start: 0.7017 (mtp180) cc_final: 0.6653 (mtp85) REVERT: A 135 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8174 (mt-10) REVERT: A 166 LYS cc_start: 0.8739 (mttt) cc_final: 0.8212 (mmtm) REVERT: B 135 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8207 (mt-10) REVERT: B 166 LYS cc_start: 0.8633 (mttt) cc_final: 0.8085 (mmtt) outliers start: 15 outliers final: 10 residues processed: 114 average time/residue: 0.1847 time to fit residues: 31.4070 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 : 1.061 ------------------------------------------------------------------------------- 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: 2.9990 chunk 76 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 109 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 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 = 0.165759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121202 restraints weight = 10855.541| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.09 r_work: 0.3246 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10010 Z= 0.140 Angle : 0.544 9.034 13636 Z= 0.285 Chirality : 0.044 0.153 1530 Planarity : 0.004 0.044 1718 Dihedral : 5.132 54.376 1370 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.42 % Favored : 95.42 % Rotamer: Outliers : 1.76 % Allowed : 10.56 % Favored : 87.69 % 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: 0.23 (0.25), residues: 1244 helix: 1.85 (0.35), residues: 196 sheet: 0.55 (0.24), residues: 544 loop : -0.95 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 33 HIS 0.004 0.001 HIS C 202 PHE 0.019 0.002 PHE F 109 TYR 0.011 0.001 TYR C 53 ARG 0.002 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 425) hydrogen bonds : angle 5.60126 ( 1128) SS BOND : bond 0.00680 ( 8) SS BOND : angle 1.26913 ( 16) covalent geometry : bond 0.00337 (10002) covalent geometry : angle 0.54282 (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 114 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.113 Fit side-chains REVERT: C 107 LYS cc_start: 0.8669 (tttt) cc_final: 0.8066 (tptt) REVERT: C 174 ASP cc_start: 0.7389 (p0) cc_final: 0.6872 (t0) REVERT: E 107 LYS cc_start: 0.8637 (tttt) cc_final: 0.8029 (tptt) REVERT: E 174 ASP cc_start: 0.7400 (p0) cc_final: 0.6848 (t0) REVERT: F 142 MET cc_start: 0.5825 (mmm) cc_final: 0.5461 (mmm) REVERT: A 107 ARG cc_start: 0.6914 (mtp180) cc_final: 0.6457 (mtp85) REVERT: A 135 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8136 (mt-10) REVERT: A 166 LYS cc_start: 0.8763 (mttt) cc_final: 0.8185 (mmtm) REVERT: B 135 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8182 (mt-10) REVERT: B 166 LYS cc_start: 0.8706 (mttt) cc_final: 0.8106 (mmtt) outliers start: 19 outliers final: 15 residues processed: 109 average time/residue: 0.1782 time to fit residues: 29.3960 Evaluate side-chains 109 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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: 2.9990 chunk 80 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** E 42 GLN F 39 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 = 0.3910 r_free = 0.3910 target = 0.163888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121506 restraints weight = 10715.925| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.15 r_work: 0.3219 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10010 Z= 0.172 Angle : 0.583 9.031 13636 Z= 0.304 Chirality : 0.045 0.160 1530 Planarity : 0.004 0.046 1718 Dihedral : 5.329 56.209 1370 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.66 % Favored : 95.18 % 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: 0.17 (0.24), residues: 1244 helix: 1.81 (0.35), residues: 196 sheet: 0.58 (0.23), residues: 542 loop : -1.08 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 33 HIS 0.004 0.001 HIS B 154 PHE 0.022 0.002 PHE F 109 TYR 0.011 0.002 TYR C 53 ARG 0.002 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.04620 ( 425) hydrogen bonds : angle 5.47805 ( 1128) SS BOND : bond 0.00786 ( 8) SS BOND : angle 1.51001 ( 16) covalent geometry : bond 0.00424 (10002) covalent geometry : angle 0.58096 (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 : 1.071 Fit side-chains REVERT: C 107 LYS cc_start: 0.8701 (tttt) cc_final: 0.8148 (tptt) REVERT: C 174 ASP cc_start: 0.7477 (p0) cc_final: 0.6975 (t0) REVERT: D 90 ASP cc_start: 0.8247 (m-30) cc_final: 0.7992 (m-30) REVERT: E 107 LYS cc_start: 0.8734 (tttt) cc_final: 0.8182 (tptt) REVERT: E 174 ASP cc_start: 0.7514 (p0) cc_final: 0.7001 (t0) REVERT: F 142 MET cc_start: 0.5982 (mmm) cc_final: 0.5618 (mmm) REVERT: A 107 ARG cc_start: 0.7000 (mtp180) cc_final: 0.6550 (mtp85) REVERT: A 135 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8162 (mt-10) REVERT: A 166 LYS cc_start: 0.8784 (mttt) cc_final: 0.8260 (mmtm) REVERT: B 135 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8193 (mt-10) REVERT: B 137 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7812 (mt-10) REVERT: B 166 LYS cc_start: 0.8710 (mttt) cc_final: 0.8193 (mmtm) outliers start: 20 outliers final: 19 residues processed: 113 average time/residue: 0.1890 time to fit residues: 31.6596 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 : 1.067 ------------------------------------------------------------------------------- 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 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 127 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.164205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122177 restraints weight = 10814.565| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.11 r_work: 0.3227 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10010 Z= 0.156 Angle : 0.559 8.628 13636 Z= 0.292 Chirality : 0.045 0.156 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.282 56.045 1370 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.34 % Favored : 95.50 % Rotamer: Outliers : 2.87 % Allowed : 10.65 % 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: 0.26 (0.24), residues: 1244 helix: 1.90 (0.35), residues: 196 sheet: 0.64 (0.24), residues: 540 loop : -1.02 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 33 HIS 0.004 0.001 HIS A 155 PHE 0.021 0.002 PHE F 109 TYR 0.010 0.001 TYR C 53 ARG 0.002 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 425) hydrogen bonds : angle 5.31224 ( 1128) SS BOND : bond 0.00678 ( 8) SS BOND : angle 1.36576 ( 16) covalent geometry : bond 0.00383 (10002) covalent geometry : angle 0.55724 (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 131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 1.031 Fit side-chains REVERT: C 107 LYS cc_start: 0.8526 (tttt) cc_final: 0.8035 (tptt) REVERT: C 174 ASP cc_start: 0.7337 (p0) cc_final: 0.6948 (t0) REVERT: E 107 LYS cc_start: 0.8587 (tttt) cc_final: 0.8055 (tptt) REVERT: E 174 ASP cc_start: 0.7330 (p0) cc_final: 0.6938 (t0) REVERT: F 65 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8270 (mtmt) REVERT: F 142 MET cc_start: 0.6083 (mmm) cc_final: 0.5753 (mmt) REVERT: A 90 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6715 (mp) REVERT: A 107 ARG cc_start: 0.6923 (mtp180) cc_final: 0.6524 (mtp85) REVERT: A 135 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8097 (mt-10) REVERT: A 166 LYS cc_start: 0.8681 (mttt) cc_final: 0.8207 (mmtm) REVERT: B 90 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6715 (mp) REVERT: B 135 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8105 (mt-10) REVERT: B 137 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7803 (mt-10) REVERT: B 166 LYS cc_start: 0.8606 (mttt) cc_final: 0.8158 (mmtm) outliers start: 31 outliers final: 24 residues processed: 120 average time/residue: 0.1982 time to fit residues: 34.6177 Evaluate side-chains 126 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 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 65 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 GLN C 42 GLN D 39 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.162037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122772 restraints weight = 10856.945| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.88 r_work: 0.3213 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10010 Z= 0.225 Angle : 0.647 8.776 13636 Z= 0.334 Chirality : 0.048 0.168 1530 Planarity : 0.005 0.045 1718 Dihedral : 5.598 58.787 1370 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.06 % Favored : 94.77 % Rotamer: Outliers : 3.24 % Allowed : 11.30 % 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 (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: 0.14 (0.24), residues: 1244 helix: 1.72 (0.35), residues: 196 sheet: 0.59 (0.24), residues: 530 loop : -1.08 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 33 HIS 0.006 0.001 HIS A 155 PHE 0.026 0.002 PHE F 109 TYR 0.011 0.002 TYR C 53 ARG 0.003 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.05027 ( 425) hydrogen bonds : angle 5.49425 ( 1128) SS BOND : bond 0.00892 ( 8) SS BOND : angle 1.80042 ( 16) covalent geometry : bond 0.00569 (10002) covalent geometry : angle 0.64463 (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 133 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.985 Fit side-chains REVERT: C 107 LYS cc_start: 0.8658 (tttt) cc_final: 0.8162 (tptt) REVERT: C 174 ASP cc_start: 0.7502 (p0) cc_final: 0.7092 (t0) REVERT: D 112 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: E 107 LYS cc_start: 0.8667 (tttt) cc_final: 0.8180 (tptt) REVERT: E 174 ASP cc_start: 0.7481 (p0) cc_final: 0.7059 (t0) REVERT: F 65 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8316 (mtmt) REVERT: F 142 MET cc_start: 0.6072 (mmm) cc_final: 0.5675 (mmt) REVERT: A 90 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6685 (mp) REVERT: A 107 ARG cc_start: 0.7040 (mtp180) cc_final: 0.6612 (mtp85) REVERT: A 135 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8157 (mt-10) REVERT: A 166 LYS cc_start: 0.8722 (mttt) cc_final: 0.8239 (mmtm) REVERT: B 90 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6708 (mp) REVERT: B 102 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8085 (tp) REVERT: B 135 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8149 (mt-10) REVERT: B 137 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8007 (mt-10) REVERT: B 166 LYS cc_start: 0.8665 (mttt) cc_final: 0.8194 (mmtm) outliers start: 35 outliers final: 27 residues processed: 121 average time/residue: 0.1841 time to fit residues: 32.9209 Evaluate side-chains 127 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.164254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122040 restraints weight = 10864.759| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.12 r_work: 0.3221 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10010 Z= 0.141 Angle : 0.555 8.496 13636 Z= 0.289 Chirality : 0.044 0.155 1530 Planarity : 0.004 0.046 1718 Dihedral : 5.331 57.609 1370 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.42 % 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: 0.30 (0.25), residues: 1244 helix: 1.90 (0.35), residues: 196 sheet: 0.69 (0.24), residues: 530 loop : -0.98 (0.27), residues: 518 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 101 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 425) hydrogen bonds : angle 5.24048 ( 1128) SS BOND : bond 0.00638 ( 8) SS BOND : angle 1.28836 ( 16) covalent geometry : bond 0.00344 (10002) covalent geometry : angle 0.55311 (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 124 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 1.147 Fit side-chains REVERT: C 107 LYS cc_start: 0.8545 (tttt) cc_final: 0.8031 (tptt) REVERT: C 174 ASP cc_start: 0.7394 (p0) cc_final: 0.6997 (t0) REVERT: D 112 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8080 (pt0) REVERT: E 107 LYS cc_start: 0.8568 (tttt) cc_final: 0.8052 (tptt) REVERT: E 174 ASP cc_start: 0.7381 (p0) cc_final: 0.6984 (t0) REVERT: F 65 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8308 (mtmt) REVERT: F 142 MET cc_start: 0.6089 (mmm) cc_final: 0.5722 (mmt) REVERT: A 90 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6630 (mp) REVERT: A 102 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7920 (tp) REVERT: A 107 ARG cc_start: 0.6908 (mtp180) cc_final: 0.6490 (mtp85) REVERT: A 135 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8078 (mt-10) REVERT: A 166 LYS cc_start: 0.8666 (mttt) cc_final: 0.8209 (mmtm) REVERT: B 90 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6590 (mp) REVERT: B 135 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 137 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7958 (mt-10) REVERT: B 166 LYS cc_start: 0.8624 (mttt) cc_final: 0.8167 (mmtm) outliers start: 28 outliers final: 23 residues processed: 113 average time/residue: 0.1912 time to fit residues: 32.5057 Evaluate side-chains 121 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.164573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126552 restraints weight = 10891.995| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.25 r_work: 0.3156 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10010 Z= 0.141 Angle : 0.553 8.500 13636 Z= 0.286 Chirality : 0.044 0.154 1530 Planarity : 0.004 0.046 1718 Dihedral : 5.265 57.813 1370 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.90 % Favored : 94.94 % 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 (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: 0.30 (0.25), residues: 1244 helix: 1.97 (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 TRP 0.012 0.001 TRP F 33 HIS 0.004 0.001 HIS A 155 PHE 0.019 0.002 PHE D 109 TYR 0.010 0.001 TYR E 53 ARG 0.002 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 425) hydrogen bonds : angle 5.16621 ( 1128) SS BOND : bond 0.00667 ( 8) SS BOND : angle 1.27806 ( 16) covalent geometry : bond 0.00345 (10002) covalent geometry : angle 0.55124 (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 126 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 1.047 Fit side-chains REVERT: C 107 LYS cc_start: 0.8639 (tttt) cc_final: 0.8113 (tptt) REVERT: C 174 ASP cc_start: 0.7463 (p0) cc_final: 0.7009 (t0) REVERT: D 112 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8112 (pt0) REVERT: E 107 LYS cc_start: 0.8671 (tttt) cc_final: 0.8133 (tptt) REVERT: E 174 ASP cc_start: 0.7385 (p0) cc_final: 0.6947 (t0) REVERT: F 65 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8315 (mtmt) REVERT: F 142 MET cc_start: 0.6087 (mmm) cc_final: 0.5705 (mmt) REVERT: A 90 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6644 (mp) REVERT: A 102 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7973 (tp) REVERT: A 107 ARG cc_start: 0.6927 (mtp180) cc_final: 0.6482 (mtp85) REVERT: A 135 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8122 (mt-10) REVERT: A 166 LYS cc_start: 0.8739 (mttt) cc_final: 0.8259 (mmtm) REVERT: B 90 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6638 (mp) REVERT: B 102 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8006 (tp) REVERT: B 135 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8157 (mt-10) REVERT: B 137 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7993 (mt-10) REVERT: B 166 LYS cc_start: 0.8679 (mttt) cc_final: 0.8202 (mmtm) outliers start: 29 outliers final: 24 residues processed: 114 average time/residue: 0.1906 time to fit residues: 32.2130 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 : 1.075 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 80 optimal weight: 0.0370 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.164152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.127392 restraints weight = 10771.829| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.35 r_work: 0.3211 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2109 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= 0.146 Angle : 0.557 8.184 13636 Z= 0.289 Chirality : 0.044 0.155 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.284 58.828 1370 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.50 % Favored : 95.34 % Rotamer: Outliers : 2.87 % Allowed : 12.13 % 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 (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: 1.98 (0.35), residues: 196 sheet: 0.60 (0.24), residues: 544 loop : -0.94 (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 0.020 0.002 PHE F 109 TYR 0.010 0.001 TYR E 53 ARG 0.002 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 425) hydrogen bonds : angle 5.14059 ( 1128) SS BOND : bond 0.00682 ( 8) SS BOND : angle 1.32941 ( 16) covalent geometry : bond 0.00360 (10002) covalent geometry : angle 0.55507 (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 124 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 1.058 Fit side-chains REVERT: C 107 LYS cc_start: 0.8688 (tttt) cc_final: 0.8118 (tptt) REVERT: C 174 ASP cc_start: 0.7472 (p0) cc_final: 0.6947 (t0) REVERT: D 112 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: E 107 LYS cc_start: 0.8726 (tttt) cc_final: 0.8142 (tptt) REVERT: E 174 ASP cc_start: 0.7369 (p0) cc_final: 0.6865 (t0) REVERT: F 65 LYS cc_start: 0.8532 (mtmt) cc_final: 0.8294 (mtmt) REVERT: F 142 MET cc_start: 0.6143 (mmm) cc_final: 0.5704 (mmt) REVERT: A 90 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6518 (mp) REVERT: A 102 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7904 (tp) REVERT: A 107 ARG cc_start: 0.6890 (mtp180) cc_final: 0.6401 (mtp85) REVERT: A 135 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8111 (mt-10) REVERT: A 166 LYS cc_start: 0.8758 (mttt) cc_final: 0.8222 (mmtm) REVERT: B 90 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6535 (mp) REVERT: B 102 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7947 (tp) REVERT: B 135 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 137 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8033 (mt-10) REVERT: B 166 LYS cc_start: 0.8689 (mttt) cc_final: 0.8164 (mmtm) outliers start: 31 outliers final: 26 residues processed: 111 average time/residue: 0.1832 time to fit residues: 30.3890 Evaluate side-chains 124 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 A residue 173 SER 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: 0.9990 chunk 106 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 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 = 0.3918 r_free = 0.3918 target = 0.164442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126789 restraints weight = 10814.875| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.03 r_work: 0.3182 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2147 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= 0.137 Angle : 0.543 8.258 13636 Z= 0.282 Chirality : 0.044 0.152 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.239 60.196 1370 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.18 % 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: 0.35 (0.25), residues: 1244 helix: 2.02 (0.35), residues: 196 sheet: 0.64 (0.24), residues: 544 loop : -0.92 (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 0.010 0.001 TYR C 53 ARG 0.002 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 425) hydrogen bonds : angle 5.08248 ( 1128) SS BOND : bond 0.00641 ( 8) SS BOND : angle 1.22231 ( 16) covalent geometry : bond 0.00336 (10002) covalent geometry : angle 0.54196 (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: 30 poor density : 95 time to evaluate : 1.173 Fit side-chains REVERT: C 107 LYS cc_start: 0.8602 (tttt) cc_final: 0.8099 (tptt) REVERT: C 174 ASP cc_start: 0.7433 (p0) cc_final: 0.7000 (t0) REVERT: D 112 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: E 107 LYS cc_start: 0.8624 (tttt) cc_final: 0.8117 (tptt) REVERT: E 174 ASP cc_start: 0.7353 (p0) cc_final: 0.6954 (t0) REVERT: F 65 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8330 (mtmt) REVERT: F 81 MET cc_start: 0.8899 (tmm) cc_final: 0.8676 (ttp) REVERT: F 142 MET cc_start: 0.6197 (mmm) cc_final: 0.5809 (mmt) REVERT: A 90 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6692 (mp) REVERT: A 102 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7978 (tp) REVERT: A 107 ARG cc_start: 0.6894 (mtp180) cc_final: 0.6470 (mtp85) REVERT: A 135 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8074 (mt-10) REVERT: A 166 LYS cc_start: 0.8710 (mttt) cc_final: 0.8259 (mmtm) REVERT: B 90 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6688 (mp) REVERT: B 102 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8009 (tp) REVERT: B 135 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8138 (mt-10) REVERT: B 137 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8010 (mt-10) REVERT: B 166 LYS cc_start: 0.8639 (mttt) cc_final: 0.8199 (mmtm) outliers start: 30 outliers final: 25 residues processed: 113 average time/residue: 0.2003 time to fit residues: 33.5638 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 : 1.086 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.163470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125914 restraints weight = 10771.413| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.00 r_work: 0.3157 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.004 0.039 10010 Z= 0.159 Angle : 0.571 8.406 13636 Z= 0.295 Chirality : 0.045 0.157 1530 Planarity : 0.004 0.045 1718 Dihedral : 5.344 61.705 1370 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.42 % Favored : 95.50 % Rotamer: Outliers : 2.87 % Allowed : 12.13 % 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 (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: 1.96 (0.35), residues: 196 sheet: 0.68 (0.24), residues: 536 loop : -0.94 (0.27), residues: 512 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 0.021 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 0.04226 ( 425) hydrogen bonds : angle 5.15014 ( 1128) SS BOND : bond 0.00721 ( 8) SS BOND : angle 1.37011 ( 16) covalent geometry : bond 0.00395 (10002) covalent geometry : angle 0.56932 (13620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5559.22 seconds wall clock time: 97 minutes 0.92 seconds (5820.92 seconds total)