Starting phenix.real_space_refine on Fri Feb 14 09:36:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6skm_10228/02_2025/6skm_10228.cif Found real_map, /net/cci-nas-00/data/ceres_data/6skm_10228/02_2025/6skm_10228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6skm_10228/02_2025/6skm_10228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6skm_10228/02_2025/6skm_10228.map" model { file = "/net/cci-nas-00/data/ceres_data/6skm_10228/02_2025/6skm_10228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6skm_10228/02_2025/6skm_10228.cif" } resolution = 4.9 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= 0.001 sd= 0.007 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 78 5.16 5 C 6508 2.51 5 N 1800 2.21 5 O 1950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "C" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "D" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "F" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Time building chain proxies: 7.91, per 1000 atoms: 0.77 Number of scatterers: 10336 At special positions: 0 Unit cell: (115.9, 111.02, 84.18, 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 78 16.00 O 1950 8.00 N 1800 7.00 C 6508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=1.53 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 198 " - pdb=" SG CYS F 218 " distance=2.19 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: 2.54 Conformation dependent library (CDL) restraints added in 1.6 seconds 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 67.0% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.511A pdb=" N GLU A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.194A pdb=" N ASN A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TRP A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'B' and resid 16 through 31 removed outlier: 3.595A pdb=" N LYS B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 removed outlier: 4.208A pdb=" N ALA B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 119 removed outlier: 3.586A pdb=" N GLN B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.524A pdb=" N ILE B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.578A pdb=" N LYS B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN B 183 " --> pdb=" O GLN B 179 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.956A pdb=" N MET B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.606A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.616A pdb=" N MET C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 removed outlier: 3.627A pdb=" N MET C 66 " --> pdb=" O HIS C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 160 through 174 removed outlier: 3.695A pdb=" N TYR C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.625A pdb=" N GLN C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 31 removed outlier: 3.548A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 110 through 119 removed outlier: 3.718A pdb=" N GLN D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 146 Processing helix chain 'D' and resid 160 through 173 Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.703A pdb=" N TRP D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 210 through 220 removed outlier: 3.533A pdb=" N GLY D 220 " --> pdb=" O THR D 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 removed outlier: 3.634A pdb=" N MET E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 removed outlier: 4.008A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 removed outlier: 4.176A pdb=" N ALA E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.648A pdb=" N GLN E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 145 Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 178 through 191 removed outlier: 4.188A pdb=" N TRP E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'E' and resid 210 through 218 removed outlier: 3.970A pdb=" N MET E 214 " --> pdb=" O THR E 210 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS E 218 " --> pdb=" O MET E 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 31 removed outlier: 3.731A pdb=" N LEU F 20 " --> pdb=" O SER F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 removed outlier: 3.546A pdb=" N MET F 66 " --> pdb=" O HIS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 119 removed outlier: 3.507A pdb=" N GLN F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 160 through 174 removed outlier: 3.554A pdb=" N TYR F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 186 Processing helix chain 'F' and resid 188 through 193 Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.617A pdb=" N GLY F 206 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.717A pdb=" N GLN F 219 " --> pdb=" O MET F 215 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 3.569A pdb=" N VAL A 3 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 11 " --> pdb=" O VAL A 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 2 through 3 removed outlier: 4.465A pdb=" N VAL C 3 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL C 11 " --> pdb=" O VAL C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 2 through 4 removed outlier: 3.794A pdb=" N VAL D 3 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL D 11 " --> pdb=" O VAL D 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 2 through 3 removed outlier: 4.588A pdb=" N VAL F 3 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL F 11 " --> pdb=" O VAL F 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 577 hydrogen bonds defined for protein. 1731 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: 2.66 Time building geometry restraints manager: 2.79 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: 2958 1.34 - 1.45: 1564 1.45 - 1.57: 5900 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 10566 Sorted by residual: bond pdb=" N PRO D 38 " pdb=" CD PRO D 38 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" N PRO A 38 " pdb=" CD PRO A 38 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" N PRO A 34 " pdb=" CD PRO A 34 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.77e+01 bond pdb=" C SER A 33 " pdb=" N PRO A 34 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.28e-02 6.10e+03 1.74e+01 bond pdb=" N PRO E 34 " pdb=" CD PRO E 34 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.73e+01 ... (remaining 10561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 14192 2.64 - 5.27: 158 5.27 - 7.91: 12 7.91 - 10.54: 0 10.54 - 13.18: 4 Bond angle restraints: 14366 Sorted by residual: angle pdb=" CA ILE D 37 " pdb=" C ILE D 37 " pdb=" N PRO D 38 " ideal model delta sigma weight residual 121.00 114.88 6.12 8.30e-01 1.45e+00 5.44e+01 angle pdb=" N GLU C 29 " pdb=" CA GLU C 29 " pdb=" C GLU C 29 " ideal model delta sigma weight residual 111.36 118.39 -7.03 1.09e+00 8.42e-01 4.15e+01 angle pdb=" N GLU B 29 " pdb=" CA GLU B 29 " pdb=" C GLU B 29 " ideal model delta sigma weight residual 111.36 118.26 -6.90 1.09e+00 8.42e-01 4.00e+01 angle pdb=" C ILE E 37 " pdb=" CA ILE E 37 " pdb=" CB ILE E 37 " ideal model delta sigma weight residual 114.35 107.81 6.54 1.06e+00 8.90e-01 3.80e+01 angle pdb=" O ILE D 37 " pdb=" C ILE D 37 " pdb=" N PRO D 38 " ideal model delta sigma weight residual 120.07 124.08 -4.01 7.10e-01 1.98e+00 3.18e+01 ... (remaining 14361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6209 17.91 - 35.83: 276 35.83 - 53.74: 31 53.74 - 71.66: 2 71.66 - 89.57: 4 Dihedral angle restraints: 6522 sinusoidal: 2704 harmonic: 3818 Sorted by residual: dihedral pdb=" CB CYS C 198 " pdb=" SG CYS C 198 " pdb=" SG CYS C 218 " pdb=" CB CYS C 218 " ideal model delta sinusoidal sigma weight residual -86.00 -13.10 -72.90 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS F 198 " pdb=" SG CYS F 198 " pdb=" SG CYS F 218 " pdb=" CB CYS F 218 " ideal model delta sinusoidal sigma weight residual -86.00 -117.93 31.93 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" C PHE E 32 " pdb=" N PHE E 32 " pdb=" CA PHE E 32 " pdb=" CB PHE E 32 " ideal model delta harmonic sigma weight residual -122.60 -130.69 8.09 0 2.50e+00 1.60e-01 1.05e+01 ... (remaining 6519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1234 0.045 - 0.090: 270 0.090 - 0.135: 79 0.135 - 0.180: 15 0.180 - 0.225: 6 Chirality restraints: 1604 Sorted by residual: chirality pdb=" CA GLU B 29 " pdb=" N GLU B 29 " pdb=" C GLU B 29 " pdb=" CB GLU B 29 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA LYS C 30 " pdb=" N LYS C 30 " pdb=" C LYS C 30 " pdb=" CB LYS C 30 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA VAL F 27 " pdb=" N VAL F 27 " pdb=" C VAL F 27 " pdb=" CB VAL F 27 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1601 not shown) Planarity restraints: 1882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 37 " -0.047 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO E 38 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 35 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C GLU F 35 " -0.035 2.00e-02 2.50e+03 pdb=" O GLU F 35 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL F 36 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 19 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C THR E 19 " 0.027 2.00e-02 2.50e+03 pdb=" O THR E 19 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU E 20 " -0.009 2.00e-02 2.50e+03 ... (remaining 1879 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 2 2.14 - 2.83: 3178 2.83 - 3.52: 14574 3.52 - 4.21: 22221 4.21 - 4.90: 38333 Nonbonded interactions: 78308 Sorted by model distance: nonbonded pdb=" O THR D 58 " pdb=" OE2 GLU E 35 " model vdw 1.449 3.040 nonbonded pdb=" O PRO F 17 " pdb=" OD1 ASN F 21 " model vdw 2.029 3.040 nonbonded pdb=" NZ LYS C 30 " pdb=" OE2 GLU C 35 " model vdw 2.202 3.120 nonbonded pdb=" O PRO F 17 " pdb=" CG ASN F 21 " model vdw 2.204 3.270 nonbonded pdb=" OH TYR D 145 " pdb=" NH2 ARG E 162 " model vdw 2.308 3.120 ... (remaining 78303 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' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'B' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'C' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'D' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'E' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'F' and (resid 1 through 17 or resid 19 through 220)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.870 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10566 Z= 0.222 Angle : 0.638 13.176 14366 Z= 0.421 Chirality : 0.044 0.225 1604 Planarity : 0.004 0.070 1882 Dihedral : 9.229 89.573 4028 Min Nonbonded Distance : 1.449 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.18 % Allowed : 5.13 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1310 helix: -0.14 (0.17), residues: 814 sheet: None (None), residues: 0 loop : -1.47 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 184 HIS 0.001 0.000 HIS F 87 PHE 0.011 0.001 PHE E 32 TYR 0.004 0.001 TYR C 164 ARG 0.001 0.000 ARG E 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 628 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7758 (tptm) REVERT: A 79 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8554 (tp30) REVERT: A 87 HIS cc_start: 0.7892 (m-70) cc_final: 0.7412 (t-90) REVERT: A 100 ARG cc_start: 0.8498 (ttt180) cc_final: 0.7971 (tmm-80) REVERT: A 103 ASP cc_start: 0.7931 (m-30) cc_final: 0.7158 (m-30) REVERT: A 128 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7956 (tm-30) REVERT: A 129 ILE cc_start: 0.8753 (mt) cc_final: 0.8366 (tt) REVERT: A 149 SER cc_start: 0.8961 (t) cc_final: 0.8650 (p) REVERT: A 152 ASP cc_start: 0.8821 (m-30) cc_final: 0.8569 (m-30) REVERT: A 187 GLU cc_start: 0.9321 (mt-10) cc_final: 0.9107 (pt0) REVERT: A 202 LEU cc_start: 0.9520 (mt) cc_final: 0.9318 (mm) REVERT: A 212 GLU cc_start: 0.8848 (mt-10) cc_final: 0.7898 (pm20) REVERT: B 39 MET cc_start: 0.9070 (tpp) cc_final: 0.8530 (tpt) REVERT: B 40 PHE cc_start: 0.8539 (t80) cc_final: 0.8257 (t80) REVERT: B 45 GLU cc_start: 0.8133 (tp30) cc_final: 0.7827 (tm-30) REVERT: B 51 ASP cc_start: 0.8584 (t0) cc_final: 0.8359 (t0) REVERT: B 68 MET cc_start: 0.8936 (mtp) cc_final: 0.8417 (tpp) REVERT: B 84 HIS cc_start: 0.8830 (m90) cc_final: 0.8428 (t-90) REVERT: B 86 VAL cc_start: 0.7380 (p) cc_final: 0.7008 (m) REVERT: B 103 ASP cc_start: 0.9097 (m-30) cc_final: 0.8585 (m-30) REVERT: B 128 GLU cc_start: 0.9299 (mp0) cc_final: 0.8763 (pp20) REVERT: B 131 LYS cc_start: 0.8533 (mtpt) cc_final: 0.7833 (mtpt) REVERT: B 141 ILE cc_start: 0.9141 (mt) cc_final: 0.8572 (mt) REVERT: B 142 VAL cc_start: 0.9447 (m) cc_final: 0.9240 (p) REVERT: B 144 MET cc_start: 0.8669 (tmm) cc_final: 0.7710 (tmm) REVERT: B 166 ASP cc_start: 0.8372 (t0) cc_final: 0.8028 (t0) REVERT: C 5 ASN cc_start: 0.7693 (t0) cc_final: 0.7048 (p0) REVERT: C 24 VAL cc_start: 0.8744 (t) cc_final: 0.8484 (p) REVERT: C 52 LEU cc_start: 0.9751 (mp) cc_final: 0.9539 (mp) REVERT: C 68 MET cc_start: 0.9313 (mtp) cc_final: 0.8908 (mtt) REVERT: C 103 ASP cc_start: 0.8661 (m-30) cc_final: 0.7833 (t0) REVERT: C 104 ILE cc_start: 0.8501 (tt) cc_final: 0.8086 (pt) REVERT: C 113 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8100 (mm-30) REVERT: C 158 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8760 (mmmm) REVERT: D 30 LYS cc_start: 0.8436 (mttm) cc_final: 0.8169 (tptp) REVERT: D 40 PHE cc_start: 0.9006 (t80) cc_final: 0.8794 (t80) REVERT: D 51 ASP cc_start: 0.8543 (m-30) cc_final: 0.8214 (m-30) REVERT: D 54 THR cc_start: 0.9115 (p) cc_final: 0.8914 (p) REVERT: D 55 MET cc_start: 0.9223 (ttm) cc_final: 0.8923 (ttm) REVERT: D 71 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8193 (mt-10) REVERT: D 115 ILE cc_start: 0.8841 (mm) cc_final: 0.8619 (mm) REVERT: D 128 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7790 (tm-30) REVERT: D 129 ILE cc_start: 0.8819 (mt) cc_final: 0.8539 (tt) REVERT: D 131 LYS cc_start: 0.9363 (tttt) cc_final: 0.9139 (ptpt) REVERT: D 141 ILE cc_start: 0.9617 (mm) cc_final: 0.9300 (tp) REVERT: D 148 THR cc_start: 0.8567 (m) cc_final: 0.7210 (m) REVERT: D 149 SER cc_start: 0.8749 (t) cc_final: 0.8142 (p) REVERT: D 171 THR cc_start: 0.9274 (p) cc_final: 0.9013 (p) REVERT: E 30 LYS cc_start: 0.9054 (mmtt) cc_final: 0.7345 (mppt) REVERT: E 68 MET cc_start: 0.8819 (mtp) cc_final: 0.8435 (mmm) REVERT: E 79 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7678 (mm-30) REVERT: E 84 HIS cc_start: 0.8672 (m90) cc_final: 0.8452 (t-90) REVERT: E 86 VAL cc_start: 0.6692 (p) cc_final: 0.6453 (m) REVERT: E 103 ASP cc_start: 0.8880 (m-30) cc_final: 0.8363 (m-30) REVERT: E 140 LYS cc_start: 0.9253 (mttt) cc_final: 0.8759 (mtpt) REVERT: E 141 ILE cc_start: 0.9157 (mt) cc_final: 0.8307 (mt) REVERT: E 211 LEU cc_start: 0.8774 (tt) cc_final: 0.8482 (tt) REVERT: F 25 LYS cc_start: 0.9659 (mttt) cc_final: 0.9308 (mtmm) REVERT: F 52 LEU cc_start: 0.9748 (mp) cc_final: 0.9307 (mp) REVERT: F 53 ASN cc_start: 0.8888 (m-40) cc_final: 0.8670 (m110) REVERT: F 62 HIS cc_start: 0.8691 (m-70) cc_final: 0.8393 (m90) REVERT: F 68 MET cc_start: 0.9413 (mtp) cc_final: 0.8723 (mtt) REVERT: F 72 THR cc_start: 0.9112 (m) cc_final: 0.8908 (p) REVERT: F 103 ASP cc_start: 0.8554 (m-30) cc_final: 0.7470 (t70) REVERT: F 115 ILE cc_start: 0.9191 (mt) cc_final: 0.8876 (pt) REVERT: F 135 ILE cc_start: 0.9178 (mt) cc_final: 0.8763 (tt) REVERT: F 138 LEU cc_start: 0.9642 (mt) cc_final: 0.9372 (mt) REVERT: F 159 GLU cc_start: 0.8983 (mp0) cc_final: 0.8762 (pt0) REVERT: F 164 TYR cc_start: 0.8694 (t80) cc_final: 0.7817 (t80) REVERT: F 184 TRP cc_start: 0.8472 (t60) cc_final: 0.8191 (t60) REVERT: F 190 LEU cc_start: 0.9313 (mt) cc_final: 0.8955 (mt) outliers start: 2 outliers final: 1 residues processed: 629 average time/residue: 0.2963 time to fit residues: 241.2573 Evaluate side-chains 382 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 7 GLN A 9 GLN A 53 ASN ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN C 5 ASN C 67 GLN C 95 GLN C 192 GLN D 4 GLN D 9 GLN D 53 ASN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN E 95 GLN E 176 GLN F 4 GLN F 95 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.091948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.064425 restraints weight = 76759.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.068144 restraints weight = 41703.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.070874 restraints weight = 27694.857| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10566 Z= 0.259 Angle : 0.660 7.556 14366 Z= 0.342 Chirality : 0.046 0.306 1604 Planarity : 0.006 0.055 1882 Dihedral : 3.421 22.311 1404 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.03 (0.22), residues: 1310 helix: 0.55 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.93 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 184 HIS 0.004 0.001 HIS E 62 PHE 0.037 0.003 PHE C 161 TYR 0.009 0.001 TYR D 169 ARG 0.006 0.001 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 485 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6925 (mmp) cc_final: 0.6179 (tpp) REVERT: A 30 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7749 (tptm) REVERT: A 40 PHE cc_start: 0.9097 (t80) cc_final: 0.8590 (t80) REVERT: A 53 ASN cc_start: 0.8547 (m-40) cc_final: 0.8294 (m-40) REVERT: A 55 MET cc_start: 0.8656 (mtp) cc_final: 0.8298 (mtp) REVERT: A 71 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8573 (mt-10) REVERT: A 87 HIS cc_start: 0.8170 (m-70) cc_final: 0.7600 (t-90) REVERT: A 100 ARG cc_start: 0.8593 (ttt180) cc_final: 0.8337 (tmm-80) REVERT: A 114 GLN cc_start: 0.8974 (pp30) cc_final: 0.8521 (pp30) REVERT: A 126 VAL cc_start: 0.6048 (t) cc_final: 0.5476 (p) REVERT: A 128 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 129 ILE cc_start: 0.8876 (mt) cc_final: 0.8515 (tt) REVERT: A 136 LEU cc_start: 0.9556 (tt) cc_final: 0.8902 (tt) REVERT: A 141 ILE cc_start: 0.9426 (mt) cc_final: 0.9080 (mt) REVERT: A 149 SER cc_start: 0.9018 (t) cc_final: 0.8674 (p) REVERT: A 168 PHE cc_start: 0.9074 (t80) cc_final: 0.8866 (t80) REVERT: A 190 LEU cc_start: 0.8547 (tp) cc_final: 0.8253 (tp) REVERT: A 212 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8688 (pm20) REVERT: B 39 MET cc_start: 0.9490 (tpp) cc_final: 0.8985 (tpt) REVERT: B 51 ASP cc_start: 0.9076 (t0) cc_final: 0.8850 (t0) REVERT: B 55 MET cc_start: 0.8761 (mtm) cc_final: 0.8332 (mtm) REVERT: B 68 MET cc_start: 0.9031 (mtp) cc_final: 0.8795 (mtp) REVERT: B 96 MET cc_start: 0.8742 (mmp) cc_final: 0.8469 (mmp) REVERT: B 103 ASP cc_start: 0.9124 (m-30) cc_final: 0.8720 (m-30) REVERT: B 115 ILE cc_start: 0.9451 (mt) cc_final: 0.9220 (mm) REVERT: B 128 GLU cc_start: 0.9577 (mp0) cc_final: 0.9332 (mp0) REVERT: B 135 ILE cc_start: 0.9283 (pt) cc_final: 0.8981 (pt) REVERT: B 170 LYS cc_start: 0.9368 (pttm) cc_final: 0.9106 (pttp) REVERT: B 182 LYS cc_start: 0.9450 (ptpt) cc_final: 0.9234 (ptpt) REVERT: B 215 MET cc_start: 0.8872 (mtm) cc_final: 0.8631 (ptp) REVERT: C 5 ASN cc_start: 0.8135 (t0) cc_final: 0.7186 (p0) REVERT: C 68 MET cc_start: 0.9417 (mtp) cc_final: 0.8914 (mtt) REVERT: C 103 ASP cc_start: 0.9213 (m-30) cc_final: 0.8169 (t0) REVERT: C 104 ILE cc_start: 0.8688 (tt) cc_final: 0.8099 (pt) REVERT: C 112 GLN cc_start: 0.9644 (tm-30) cc_final: 0.9437 (tm-30) REVERT: C 113 GLU cc_start: 0.9390 (mt-10) cc_final: 0.8137 (mm-30) REVERT: C 158 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8849 (mmmm) REVERT: C 168 PHE cc_start: 0.9510 (t80) cc_final: 0.9228 (t80) REVERT: D 10 MET cc_start: 0.6537 (mmp) cc_final: 0.5961 (tpp) REVERT: D 40 PHE cc_start: 0.9040 (t80) cc_final: 0.8672 (t80) REVERT: D 53 ASN cc_start: 0.8400 (m-40) cc_final: 0.8119 (m110) REVERT: D 55 MET cc_start: 0.9636 (ttm) cc_final: 0.9388 (ttt) REVERT: D 100 ARG cc_start: 0.9068 (ttt180) cc_final: 0.8332 (tmm-80) REVERT: D 103 ASP cc_start: 0.9077 (m-30) cc_final: 0.8171 (m-30) REVERT: D 126 VAL cc_start: 0.6819 (t) cc_final: 0.6619 (p) REVERT: D 128 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8034 (tm-30) REVERT: D 129 ILE cc_start: 0.9048 (mt) cc_final: 0.8707 (tt) REVERT: D 131 LYS cc_start: 0.9486 (tttt) cc_final: 0.9239 (ptpt) REVERT: D 164 TYR cc_start: 0.8266 (t80) cc_final: 0.7913 (t80) REVERT: D 168 PHE cc_start: 0.8945 (t80) cc_final: 0.8740 (t80) REVERT: D 212 GLU cc_start: 0.8990 (pt0) cc_final: 0.8587 (pm20) REVERT: E 68 MET cc_start: 0.8886 (mtp) cc_final: 0.8422 (tpp) REVERT: E 84 HIS cc_start: 0.9314 (m90) cc_final: 0.8719 (t-90) REVERT: E 96 MET cc_start: 0.8345 (mmp) cc_final: 0.7835 (mmp) REVERT: E 115 ILE cc_start: 0.9791 (mm) cc_final: 0.9352 (mm) REVERT: E 140 LYS cc_start: 0.9282 (mttt) cc_final: 0.8973 (mtpt) REVERT: E 141 ILE cc_start: 0.9006 (mt) cc_final: 0.8664 (mt) REVERT: E 144 MET cc_start: 0.8426 (ppp) cc_final: 0.8142 (ppp) REVERT: E 211 LEU cc_start: 0.9350 (tt) cc_final: 0.8991 (tt) REVERT: E 215 MET cc_start: 0.8990 (mmp) cc_final: 0.8710 (mmp) REVERT: F 62 HIS cc_start: 0.8665 (m-70) cc_final: 0.8401 (m90) REVERT: F 68 MET cc_start: 0.9430 (mtp) cc_final: 0.8997 (mtt) REVERT: F 103 ASP cc_start: 0.9074 (m-30) cc_final: 0.7959 (t0) REVERT: F 104 ILE cc_start: 0.8664 (tt) cc_final: 0.8356 (pt) REVERT: F 118 MET cc_start: 0.7624 (mmp) cc_final: 0.7350 (mmp) REVERT: F 164 TYR cc_start: 0.8547 (t80) cc_final: 0.7711 (t80) REVERT: F 167 ARG cc_start: 0.9203 (ptp90) cc_final: 0.8381 (ptp90) REVERT: F 168 PHE cc_start: 0.9364 (t80) cc_final: 0.9008 (t80) REVERT: F 185 MET cc_start: 0.8850 (mmp) cc_final: 0.8557 (mmm) REVERT: F 190 LEU cc_start: 0.9403 (mt) cc_final: 0.8813 (mt) outliers start: 1 outliers final: 0 residues processed: 486 average time/residue: 0.2722 time to fit residues: 174.8635 Evaluate side-chains 343 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 93 optimal weight: 0.0770 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 84 HIS C 95 GLN D 74 ASN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.088511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.060420 restraints weight = 82214.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.064051 restraints weight = 44017.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.066772 restraints weight = 29402.413| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10566 Z= 0.252 Angle : 0.641 6.382 14366 Z= 0.335 Chirality : 0.045 0.253 1604 Planarity : 0.005 0.049 1882 Dihedral : 3.742 19.244 1404 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.18 % Allowed : 2.65 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.22), residues: 1310 helix: 0.75 (0.17), residues: 838 sheet: None (None), residues: 0 loop : -0.69 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 133 HIS 0.005 0.001 HIS B 84 PHE 0.032 0.002 PHE C 161 TYR 0.013 0.002 TYR B 169 ARG 0.006 0.001 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 441 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.7085 (mmp) cc_final: 0.6291 (tpp) REVERT: A 29 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7971 (pt0) REVERT: A 30 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7724 (tptm) REVERT: A 40 PHE cc_start: 0.9138 (t80) cc_final: 0.8626 (t80) REVERT: A 53 ASN cc_start: 0.8632 (m-40) cc_final: 0.8260 (m110) REVERT: A 68 MET cc_start: 0.9288 (ppp) cc_final: 0.8859 (ppp) REVERT: A 71 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8501 (mt-10) REVERT: A 87 HIS cc_start: 0.8277 (m-70) cc_final: 0.7718 (t70) REVERT: A 113 GLU cc_start: 0.9330 (mt-10) cc_final: 0.9082 (tt0) REVERT: A 114 GLN cc_start: 0.8885 (pp30) cc_final: 0.8621 (pp30) REVERT: A 132 ARG cc_start: 0.9271 (tmt-80) cc_final: 0.8870 (tpt90) REVERT: A 136 LEU cc_start: 0.9494 (tt) cc_final: 0.9028 (tt) REVERT: A 139 ASN cc_start: 0.8891 (t0) cc_final: 0.8666 (t0) REVERT: A 149 SER cc_start: 0.9058 (t) cc_final: 0.8565 (p) REVERT: A 152 ASP cc_start: 0.9010 (m-30) cc_final: 0.8738 (m-30) REVERT: A 164 TYR cc_start: 0.8275 (t80) cc_final: 0.7995 (t80) REVERT: A 203 LYS cc_start: 0.9267 (mttt) cc_final: 0.8930 (mttt) REVERT: A 212 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8356 (pm20) REVERT: B 39 MET cc_start: 0.9558 (tpp) cc_final: 0.8958 (tpt) REVERT: B 51 ASP cc_start: 0.9157 (t0) cc_final: 0.8731 (t0) REVERT: B 55 MET cc_start: 0.8865 (mtm) cc_final: 0.8302 (mtm) REVERT: B 68 MET cc_start: 0.9071 (mtp) cc_final: 0.8773 (mtp) REVERT: B 84 HIS cc_start: 0.9463 (m90) cc_final: 0.8631 (t-90) REVERT: B 96 MET cc_start: 0.8859 (mmp) cc_final: 0.8217 (mpp) REVERT: B 103 ASP cc_start: 0.9197 (m-30) cc_final: 0.8788 (m-30) REVERT: B 112 GLN cc_start: 0.9749 (tp40) cc_final: 0.9458 (tp-100) REVERT: B 135 ILE cc_start: 0.9346 (pt) cc_final: 0.9118 (pt) REVERT: C 52 LEU cc_start: 0.9594 (mp) cc_final: 0.9373 (mp) REVERT: C 68 MET cc_start: 0.9354 (mtp) cc_final: 0.9068 (mtt) REVERT: C 103 ASP cc_start: 0.9148 (m-30) cc_final: 0.7838 (t0) REVERT: C 104 ILE cc_start: 0.8545 (tt) cc_final: 0.8095 (pt) REVERT: C 113 GLU cc_start: 0.9463 (mt-10) cc_final: 0.9019 (tt0) REVERT: C 158 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8831 (mmmm) REVERT: C 167 ARG cc_start: 0.9419 (ptp90) cc_final: 0.8529 (ptp90) REVERT: C 168 PHE cc_start: 0.9483 (t80) cc_final: 0.9231 (t80) REVERT: D 23 TRP cc_start: 0.8780 (t-100) cc_final: 0.8549 (t-100) REVERT: D 40 PHE cc_start: 0.9175 (t80) cc_final: 0.8591 (t80) REVERT: D 53 ASN cc_start: 0.8532 (m-40) cc_final: 0.8212 (m110) REVERT: D 100 ARG cc_start: 0.8871 (ttt180) cc_final: 0.8602 (tmm-80) REVERT: D 114 GLN cc_start: 0.9483 (pt0) cc_final: 0.9218 (pp30) REVERT: D 118 MET cc_start: 0.8970 (ptp) cc_final: 0.8736 (mmm) REVERT: D 128 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7917 (tm-30) REVERT: D 129 ILE cc_start: 0.9108 (mt) cc_final: 0.8759 (tt) REVERT: D 131 LYS cc_start: 0.9491 (tttt) cc_final: 0.9252 (ptpt) REVERT: D 144 MET cc_start: 0.9361 (ttt) cc_final: 0.8931 (ttt) REVERT: D 164 TYR cc_start: 0.8348 (t80) cc_final: 0.8053 (t80) REVERT: D 169 TYR cc_start: 0.9102 (m-80) cc_final: 0.8559 (m-80) REVERT: D 212 GLU cc_start: 0.9138 (pt0) cc_final: 0.8538 (pm20) REVERT: E 28 GLU cc_start: 0.9024 (pt0) cc_final: 0.8609 (pp20) REVERT: E 35 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7986 (tm-30) REVERT: E 68 MET cc_start: 0.8886 (mtp) cc_final: 0.8546 (tpp) REVERT: E 84 HIS cc_start: 0.9464 (m90) cc_final: 0.8820 (t-90) REVERT: E 96 MET cc_start: 0.8409 (mmp) cc_final: 0.7780 (mpp) REVERT: E 103 ASP cc_start: 0.8952 (m-30) cc_final: 0.8544 (m-30) REVERT: E 124 ILE cc_start: 0.8604 (mp) cc_final: 0.7748 (mp) REVERT: E 140 LYS cc_start: 0.9337 (mttt) cc_final: 0.9053 (mtpt) REVERT: E 141 ILE cc_start: 0.9124 (mt) cc_final: 0.8773 (mt) REVERT: E 144 MET cc_start: 0.8528 (ppp) cc_final: 0.8094 (ppp) REVERT: E 145 TYR cc_start: 0.8392 (t80) cc_final: 0.8168 (t80) REVERT: F 52 LEU cc_start: 0.9832 (mp) cc_final: 0.9573 (mp) REVERT: F 68 MET cc_start: 0.9398 (mtp) cc_final: 0.9074 (mtt) REVERT: F 103 ASP cc_start: 0.9075 (m-30) cc_final: 0.8069 (t70) REVERT: F 104 ILE cc_start: 0.8829 (tt) cc_final: 0.8472 (pt) REVERT: F 164 TYR cc_start: 0.8690 (t80) cc_final: 0.7756 (t80) REVERT: F 167 ARG cc_start: 0.9276 (ptp90) cc_final: 0.8473 (ptp90) REVERT: F 168 PHE cc_start: 0.9484 (t80) cc_final: 0.9088 (t80) REVERT: F 190 LEU cc_start: 0.9476 (mt) cc_final: 0.8813 (mt) outliers start: 2 outliers final: 0 residues processed: 443 average time/residue: 0.2707 time to fit residues: 161.5471 Evaluate side-chains 333 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 39 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 55 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 74 ASN ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN C 95 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 192 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.087125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.060370 restraints weight = 68978.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.063721 restraints weight = 39387.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.066214 restraints weight = 26911.357| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10566 Z= 0.241 Angle : 0.640 8.568 14366 Z= 0.336 Chirality : 0.046 0.206 1604 Planarity : 0.005 0.046 1882 Dihedral : 3.975 18.800 1404 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.18 % Allowed : 1.95 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.22), residues: 1310 helix: 0.77 (0.17), residues: 836 sheet: None (None), residues: 0 loop : -0.56 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 80 HIS 0.005 0.001 HIS D 62 PHE 0.025 0.002 PHE C 161 TYR 0.021 0.002 TYR B 145 ARG 0.018 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 411 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7997 (pt0) REVERT: A 30 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7777 (tptm) REVERT: A 40 PHE cc_start: 0.9109 (t80) cc_final: 0.8583 (t80) REVERT: A 53 ASN cc_start: 0.8686 (m-40) cc_final: 0.8313 (m110) REVERT: A 68 MET cc_start: 0.9311 (ppp) cc_final: 0.8811 (ppp) REVERT: A 71 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8640 (mt-10) REVERT: A 100 ARG cc_start: 0.8571 (ttt180) cc_final: 0.8359 (tmm-80) REVERT: A 132 ARG cc_start: 0.9315 (tmt-80) cc_final: 0.8878 (tpt90) REVERT: A 136 LEU cc_start: 0.9511 (tt) cc_final: 0.9081 (tt) REVERT: A 139 ASN cc_start: 0.8820 (t0) cc_final: 0.8582 (t0) REVERT: A 149 SER cc_start: 0.9092 (t) cc_final: 0.8659 (p) REVERT: A 152 ASP cc_start: 0.8973 (m-30) cc_final: 0.8707 (m-30) REVERT: A 167 ARG cc_start: 0.9584 (mpp-170) cc_final: 0.9289 (ptt-90) REVERT: A 203 LYS cc_start: 0.9325 (mttt) cc_final: 0.8994 (mttt) REVERT: A 212 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8389 (pm20) REVERT: B 51 ASP cc_start: 0.9137 (t0) cc_final: 0.8731 (t0) REVERT: B 55 MET cc_start: 0.8989 (mtm) cc_final: 0.8163 (mtm) REVERT: B 68 MET cc_start: 0.9016 (mtp) cc_final: 0.8558 (tpp) REVERT: B 84 HIS cc_start: 0.9485 (m90) cc_final: 0.8793 (t-90) REVERT: B 96 MET cc_start: 0.8987 (mmp) cc_final: 0.8373 (mpp) REVERT: B 103 ASP cc_start: 0.9209 (m-30) cc_final: 0.8824 (m-30) REVERT: B 112 GLN cc_start: 0.9746 (tp40) cc_final: 0.9408 (tp-100) REVERT: B 215 MET cc_start: 0.8823 (mtm) cc_final: 0.8619 (mtm) REVERT: C 52 LEU cc_start: 0.9606 (mp) cc_final: 0.9389 (mp) REVERT: C 68 MET cc_start: 0.9360 (mtp) cc_final: 0.9041 (mtt) REVERT: C 103 ASP cc_start: 0.9144 (m-30) cc_final: 0.8705 (m-30) REVERT: C 104 ILE cc_start: 0.8630 (tt) cc_final: 0.8196 (pt) REVERT: C 140 LYS cc_start: 0.9459 (mtpp) cc_final: 0.9219 (mtpp) REVERT: C 152 ASP cc_start: 0.9215 (m-30) cc_final: 0.8956 (m-30) REVERT: C 158 LYS cc_start: 0.9153 (mmmt) cc_final: 0.8853 (mmmm) REVERT: C 167 ARG cc_start: 0.9441 (ptp90) cc_final: 0.8564 (ptp90) REVERT: C 168 PHE cc_start: 0.9463 (t80) cc_final: 0.9196 (t80) REVERT: C 182 LYS cc_start: 0.8440 (ptpt) cc_final: 0.8207 (ptpt) REVERT: C 190 LEU cc_start: 0.9442 (mt) cc_final: 0.9229 (mt) REVERT: D 10 MET cc_start: 0.6944 (mmp) cc_final: 0.5890 (tpp) REVERT: D 40 PHE cc_start: 0.9194 (t80) cc_final: 0.8679 (t80) REVERT: D 53 ASN cc_start: 0.8601 (m-40) cc_final: 0.8267 (m110) REVERT: D 114 GLN cc_start: 0.9454 (pt0) cc_final: 0.9171 (pp30) REVERT: D 118 MET cc_start: 0.9018 (ptp) cc_final: 0.8808 (mmm) REVERT: D 128 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7888 (tm-30) REVERT: D 129 ILE cc_start: 0.9040 (mt) cc_final: 0.8702 (tt) REVERT: D 131 LYS cc_start: 0.9497 (tttt) cc_final: 0.9278 (ptpt) REVERT: D 164 TYR cc_start: 0.8642 (t80) cc_final: 0.8006 (t80) REVERT: D 169 TYR cc_start: 0.9181 (m-80) cc_final: 0.8798 (m-80) REVERT: D 212 GLU cc_start: 0.9129 (pt0) cc_final: 0.8572 (pm20) REVERT: E 35 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8104 (tm-30) REVERT: E 55 MET cc_start: 0.9625 (ttt) cc_final: 0.9154 (ttt) REVERT: E 68 MET cc_start: 0.8832 (mtp) cc_final: 0.8539 (tpp) REVERT: E 84 HIS cc_start: 0.9444 (m90) cc_final: 0.8803 (t-90) REVERT: E 96 MET cc_start: 0.8601 (mmp) cc_final: 0.7282 (mpp) REVERT: E 140 LYS cc_start: 0.9373 (mttt) cc_final: 0.9053 (mtpt) REVERT: E 141 ILE cc_start: 0.9184 (mt) cc_final: 0.8832 (mt) REVERT: E 144 MET cc_start: 0.8509 (ppp) cc_final: 0.8029 (ppp) REVERT: F 52 LEU cc_start: 0.9813 (mp) cc_final: 0.9580 (mp) REVERT: F 68 MET cc_start: 0.9346 (mtp) cc_final: 0.9084 (mtt) REVERT: F 118 MET cc_start: 0.7674 (mmp) cc_final: 0.7328 (mmm) REVERT: F 139 ASN cc_start: 0.9512 (t0) cc_final: 0.9288 (m-40) REVERT: F 164 TYR cc_start: 0.8752 (t80) cc_final: 0.7764 (t80) REVERT: F 167 ARG cc_start: 0.9299 (ptp90) cc_final: 0.8466 (ptp90) REVERT: F 168 PHE cc_start: 0.9535 (t80) cc_final: 0.9103 (t80) REVERT: F 185 MET cc_start: 0.8969 (mmp) cc_final: 0.8688 (mmm) REVERT: F 190 LEU cc_start: 0.9443 (mt) cc_final: 0.8767 (mt) REVERT: F 213 GLU cc_start: 0.9097 (pt0) cc_final: 0.8855 (pt0) REVERT: F 215 MET cc_start: 0.9469 (tmm) cc_final: 0.9259 (tmm) outliers start: 2 outliers final: 0 residues processed: 413 average time/residue: 0.2638 time to fit residues: 145.4882 Evaluate side-chains 319 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 40 optimal weight: 0.0040 chunk 8 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 95 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.3422 r_free = 0.3422 target = 0.086720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.060046 restraints weight = 72243.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.063500 restraints weight = 40580.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.066062 restraints weight = 27465.404| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10566 Z= 0.203 Angle : 0.632 7.187 14366 Z= 0.329 Chirality : 0.047 0.341 1604 Planarity : 0.005 0.048 1882 Dihedral : 4.056 19.826 1404 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.18 % Allowed : 1.86 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.42 (0.22), residues: 1310 helix: 0.78 (0.17), residues: 850 sheet: None (None), residues: 0 loop : -0.52 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 23 HIS 0.004 0.001 HIS D 62 PHE 0.040 0.002 PHE E 168 TYR 0.014 0.002 TYR B 169 ARG 0.011 0.001 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 408 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8051 (mt-10) REVERT: A 30 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7774 (tptm) REVERT: A 40 PHE cc_start: 0.9054 (t80) cc_final: 0.8587 (t80) REVERT: A 53 ASN cc_start: 0.8680 (m-40) cc_final: 0.8320 (m110) REVERT: A 68 MET cc_start: 0.9317 (ppp) cc_final: 0.8858 (ppp) REVERT: A 71 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8544 (mt-10) REVERT: A 100 ARG cc_start: 0.8728 (ttt180) cc_final: 0.8131 (tmm-80) REVERT: A 103 ASP cc_start: 0.9142 (m-30) cc_final: 0.8230 (m-30) REVERT: A 132 ARG cc_start: 0.9267 (tmt-80) cc_final: 0.8849 (tpt90) REVERT: A 136 LEU cc_start: 0.9477 (tt) cc_final: 0.9053 (tt) REVERT: A 139 ASN cc_start: 0.8771 (t0) cc_final: 0.8518 (t0) REVERT: A 149 SER cc_start: 0.9131 (t) cc_final: 0.8714 (p) REVERT: A 152 ASP cc_start: 0.9033 (m-30) cc_final: 0.8759 (m-30) REVERT: A 167 ARG cc_start: 0.9505 (mpp-170) cc_final: 0.9144 (ptt-90) REVERT: A 203 LYS cc_start: 0.9313 (mttt) cc_final: 0.8992 (mttt) REVERT: A 212 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8492 (pm20) REVERT: B 39 MET cc_start: 0.9572 (tpp) cc_final: 0.9154 (tmm) REVERT: B 51 ASP cc_start: 0.9086 (t0) cc_final: 0.8625 (t0) REVERT: B 55 MET cc_start: 0.9275 (mtm) cc_final: 0.8084 (mtm) REVERT: B 84 HIS cc_start: 0.9485 (m90) cc_final: 0.8799 (t-90) REVERT: B 96 MET cc_start: 0.9056 (mmp) cc_final: 0.8534 (mpp) REVERT: B 103 ASP cc_start: 0.9222 (m-30) cc_final: 0.8862 (m-30) REVERT: B 112 GLN cc_start: 0.9733 (tp40) cc_final: 0.9367 (tp-100) REVERT: B 215 MET cc_start: 0.8764 (mtm) cc_final: 0.8554 (mtm) REVERT: C 52 LEU cc_start: 0.9631 (mp) cc_final: 0.9382 (mp) REVERT: C 68 MET cc_start: 0.9371 (mtp) cc_final: 0.8999 (mtt) REVERT: C 103 ASP cc_start: 0.9102 (m-30) cc_final: 0.7955 (t70) REVERT: C 104 ILE cc_start: 0.8677 (tt) cc_final: 0.8236 (pt) REVERT: C 110 THR cc_start: 0.9506 (m) cc_final: 0.9222 (p) REVERT: C 138 LEU cc_start: 0.9783 (mt) cc_final: 0.9572 (mt) REVERT: C 140 LYS cc_start: 0.9462 (mtpp) cc_final: 0.9224 (mtpp) REVERT: C 151 LEU cc_start: 0.9426 (mm) cc_final: 0.9110 (mm) REVERT: C 158 LYS cc_start: 0.9177 (mmmt) cc_final: 0.8814 (mmmm) REVERT: C 168 PHE cc_start: 0.9502 (t80) cc_final: 0.9115 (t80) REVERT: C 182 LYS cc_start: 0.8422 (ptpt) cc_final: 0.8175 (ptpt) REVERT: C 190 LEU cc_start: 0.9426 (mt) cc_final: 0.9142 (mt) REVERT: D 40 PHE cc_start: 0.9044 (t80) cc_final: 0.8612 (t80) REVERT: D 53 ASN cc_start: 0.8581 (m-40) cc_final: 0.8231 (m110) REVERT: D 96 MET cc_start: 0.0679 (mmt) cc_final: 0.0308 (mpp) REVERT: D 100 ARG cc_start: 0.8829 (ttt180) cc_final: 0.8205 (ttm-80) REVERT: D 128 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7891 (tm-30) REVERT: D 129 ILE cc_start: 0.9034 (mt) cc_final: 0.8715 (tt) REVERT: D 131 LYS cc_start: 0.9442 (tttt) cc_final: 0.9199 (ptpt) REVERT: D 136 LEU cc_start: 0.9664 (tt) cc_final: 0.9166 (tt) REVERT: D 145 TYR cc_start: 0.7804 (m-10) cc_final: 0.7489 (m-80) REVERT: D 164 TYR cc_start: 0.8625 (t80) cc_final: 0.8013 (t80) REVERT: D 168 PHE cc_start: 0.9140 (t80) cc_final: 0.8930 (t80) REVERT: D 169 TYR cc_start: 0.9144 (m-80) cc_final: 0.8689 (m-80) REVERT: D 212 GLU cc_start: 0.9036 (pt0) cc_final: 0.8455 (pm20) REVERT: E 28 GLU cc_start: 0.9051 (pt0) cc_final: 0.8554 (pp20) REVERT: E 35 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8116 (tm-30) REVERT: E 68 MET cc_start: 0.8837 (mtp) cc_final: 0.8559 (tpp) REVERT: E 84 HIS cc_start: 0.9473 (m90) cc_final: 0.8857 (t-90) REVERT: E 96 MET cc_start: 0.8612 (mmp) cc_final: 0.7534 (mpp) REVERT: E 103 ASP cc_start: 0.9098 (m-30) cc_final: 0.8864 (m-30) REVERT: E 115 ILE cc_start: 0.9795 (mm) cc_final: 0.9385 (mm) REVERT: E 140 LYS cc_start: 0.9453 (mttt) cc_final: 0.9140 (mtpt) REVERT: E 141 ILE cc_start: 0.9166 (mt) cc_final: 0.8795 (mt) REVERT: E 144 MET cc_start: 0.8550 (ppp) cc_final: 0.8063 (ppp) REVERT: E 170 LYS cc_start: 0.9175 (pttt) cc_final: 0.8920 (pttm) REVERT: E 215 MET cc_start: 0.8919 (mtm) cc_final: 0.8718 (ptp) REVERT: F 52 LEU cc_start: 0.9817 (mp) cc_final: 0.9599 (mp) REVERT: F 68 MET cc_start: 0.9296 (mtp) cc_final: 0.8952 (mtt) REVERT: F 118 MET cc_start: 0.7775 (mmp) cc_final: 0.7417 (mmm) REVERT: F 139 ASN cc_start: 0.9485 (t0) cc_final: 0.9265 (m-40) REVERT: F 164 TYR cc_start: 0.8702 (t80) cc_final: 0.8207 (t80) REVERT: F 168 PHE cc_start: 0.9545 (t80) cc_final: 0.9103 (t80) REVERT: F 185 MET cc_start: 0.8909 (mmp) cc_final: 0.8698 (mmm) REVERT: F 190 LEU cc_start: 0.9355 (mt) cc_final: 0.8629 (mt) REVERT: F 213 GLU cc_start: 0.9133 (pt0) cc_final: 0.8927 (pt0) outliers start: 2 outliers final: 0 residues processed: 410 average time/residue: 0.2599 time to fit residues: 142.3042 Evaluate side-chains 324 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.083576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.056895 restraints weight = 81983.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.060377 restraints weight = 43558.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.062990 restraints weight = 28912.023| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10566 Z= 0.247 Angle : 0.665 8.000 14366 Z= 0.349 Chirality : 0.046 0.188 1604 Planarity : 0.005 0.053 1882 Dihedral : 4.167 19.169 1404 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.18 % Allowed : 1.68 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.22), residues: 1310 helix: 0.61 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -0.40 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 23 HIS 0.005 0.002 HIS D 62 PHE 0.021 0.002 PHE B 40 TYR 0.017 0.002 TYR B 169 ARG 0.013 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 407 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.7337 (mmp) cc_final: 0.6714 (tpp) REVERT: A 29 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8101 (mt-10) REVERT: A 30 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7719 (tptm) REVERT: A 40 PHE cc_start: 0.9104 (t80) cc_final: 0.8698 (t80) REVERT: A 53 ASN cc_start: 0.8778 (m-40) cc_final: 0.8433 (m110) REVERT: A 68 MET cc_start: 0.9359 (ppp) cc_final: 0.8936 (ppp) REVERT: A 71 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8679 (mt-10) REVERT: A 100 ARG cc_start: 0.8812 (ttt180) cc_final: 0.8236 (tmm-80) REVERT: A 103 ASP cc_start: 0.9187 (m-30) cc_final: 0.8265 (m-30) REVERT: A 131 LYS cc_start: 0.9393 (ptpp) cc_final: 0.9167 (pttt) REVERT: A 132 ARG cc_start: 0.9330 (tmt-80) cc_final: 0.8899 (tpt90) REVERT: A 136 LEU cc_start: 0.9503 (tt) cc_final: 0.9112 (tt) REVERT: A 139 ASN cc_start: 0.8833 (t0) cc_final: 0.8599 (t0) REVERT: A 149 SER cc_start: 0.9240 (t) cc_final: 0.8809 (p) REVERT: A 152 ASP cc_start: 0.9153 (m-30) cc_final: 0.8843 (m-30) REVERT: A 203 LYS cc_start: 0.9336 (mttt) cc_final: 0.9012 (mttt) REVERT: B 28 GLU cc_start: 0.8975 (pt0) cc_final: 0.8759 (pt0) REVERT: B 39 MET cc_start: 0.9610 (tpp) cc_final: 0.9193 (tmm) REVERT: B 51 ASP cc_start: 0.9237 (t0) cc_final: 0.8761 (t0) REVERT: B 55 MET cc_start: 0.9314 (mtm) cc_final: 0.8206 (mtm) REVERT: B 68 MET cc_start: 0.9115 (ttm) cc_final: 0.8644 (tpp) REVERT: B 84 HIS cc_start: 0.9514 (m90) cc_final: 0.9167 (m170) REVERT: B 96 MET cc_start: 0.9114 (mmp) cc_final: 0.8643 (mpp) REVERT: B 103 ASP cc_start: 0.9258 (m-30) cc_final: 0.8994 (m-30) REVERT: B 112 GLN cc_start: 0.9757 (tp40) cc_final: 0.9405 (tp-100) REVERT: B 215 MET cc_start: 0.8853 (mtm) cc_final: 0.8570 (mtm) REVERT: C 52 LEU cc_start: 0.9711 (mp) cc_final: 0.9454 (mp) REVERT: C 68 MET cc_start: 0.9347 (mtp) cc_final: 0.8993 (mtt) REVERT: C 103 ASP cc_start: 0.9111 (m-30) cc_final: 0.8000 (t70) REVERT: C 104 ILE cc_start: 0.8787 (tt) cc_final: 0.8360 (pt) REVERT: C 128 GLU cc_start: 0.9595 (mp0) cc_final: 0.9356 (mp0) REVERT: C 140 LYS cc_start: 0.9491 (mtpp) cc_final: 0.9263 (mtpp) REVERT: C 152 ASP cc_start: 0.9107 (m-30) cc_final: 0.8825 (m-30) REVERT: C 158 LYS cc_start: 0.9219 (mmmt) cc_final: 0.8868 (mmmm) REVERT: C 168 PHE cc_start: 0.9520 (t80) cc_final: 0.9154 (t80) REVERT: C 190 LEU cc_start: 0.9434 (mt) cc_final: 0.9218 (mt) REVERT: D 53 ASN cc_start: 0.8675 (m-40) cc_final: 0.8335 (m110) REVERT: D 55 MET cc_start: 0.9339 (ttt) cc_final: 0.9058 (tmm) REVERT: D 96 MET cc_start: 0.1250 (mmt) cc_final: 0.0865 (mpp) REVERT: D 103 ASP cc_start: 0.9322 (m-30) cc_final: 0.9065 (m-30) REVERT: D 129 ILE cc_start: 0.9084 (mt) cc_final: 0.8772 (tt) REVERT: D 132 ARG cc_start: 0.9283 (tmt-80) cc_final: 0.8905 (tpt90) REVERT: D 136 LEU cc_start: 0.9630 (tt) cc_final: 0.9236 (tt) REVERT: D 141 ILE cc_start: 0.9709 (mm) cc_final: 0.9051 (mm) REVERT: D 145 TYR cc_start: 0.7875 (m-10) cc_final: 0.7671 (m-80) REVERT: D 161 PHE cc_start: 0.8229 (t80) cc_final: 0.7972 (t80) REVERT: D 168 PHE cc_start: 0.9195 (t80) cc_final: 0.8987 (t80) REVERT: D 169 TYR cc_start: 0.9182 (m-80) cc_final: 0.8808 (m-80) REVERT: D 203 LYS cc_start: 0.9475 (mttt) cc_final: 0.9134 (mttt) REVERT: D 205 LEU cc_start: 0.8584 (mt) cc_final: 0.8373 (mt) REVERT: D 212 GLU cc_start: 0.9053 (pt0) cc_final: 0.8833 (pm20) REVERT: D 215 MET cc_start: 0.8799 (ptm) cc_final: 0.8515 (ppp) REVERT: E 35 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8252 (tm-30) REVERT: E 68 MET cc_start: 0.8773 (mtp) cc_final: 0.8466 (tpp) REVERT: E 79 GLU cc_start: 0.9127 (pp20) cc_final: 0.8879 (pp20) REVERT: E 84 HIS cc_start: 0.9441 (m90) cc_final: 0.8794 (t-90) REVERT: E 96 MET cc_start: 0.8725 (mmp) cc_final: 0.7764 (mpp) REVERT: E 132 ARG cc_start: 0.9281 (ptp-110) cc_final: 0.8997 (ptp-170) REVERT: E 140 LYS cc_start: 0.9433 (mttt) cc_final: 0.9147 (mtpt) REVERT: E 141 ILE cc_start: 0.9297 (mt) cc_final: 0.9025 (mt) REVERT: E 144 MET cc_start: 0.8636 (ppp) cc_final: 0.8118 (ppp) REVERT: E 170 LYS cc_start: 0.9184 (pttt) cc_final: 0.8718 (pttt) REVERT: E 215 MET cc_start: 0.8910 (mtm) cc_final: 0.8631 (ptp) REVERT: F 52 LEU cc_start: 0.9833 (mp) cc_final: 0.9514 (mp) REVERT: F 68 MET cc_start: 0.9320 (mtp) cc_final: 0.9092 (mtt) REVERT: F 104 ILE cc_start: 0.8863 (tt) cc_final: 0.8504 (pt) REVERT: F 118 MET cc_start: 0.7958 (mmp) cc_final: 0.7649 (mmm) REVERT: F 139 ASN cc_start: 0.9491 (t0) cc_final: 0.9278 (m-40) REVERT: F 164 TYR cc_start: 0.8779 (t80) cc_final: 0.7753 (t80) REVERT: F 167 ARG cc_start: 0.9384 (ptp90) cc_final: 0.8515 (ptp90) REVERT: F 168 PHE cc_start: 0.9569 (t80) cc_final: 0.9051 (t80) REVERT: F 185 MET cc_start: 0.9051 (mmp) cc_final: 0.8848 (mmm) REVERT: F 190 LEU cc_start: 0.9363 (mt) cc_final: 0.8597 (mt) REVERT: F 213 GLU cc_start: 0.9160 (pt0) cc_final: 0.8932 (pt0) outliers start: 2 outliers final: 0 residues processed: 409 average time/residue: 0.2583 time to fit residues: 140.8762 Evaluate side-chains 321 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 13 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.083892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.057467 restraints weight = 78015.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.060913 restraints weight = 42480.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.063452 restraints weight = 28394.910| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10566 Z= 0.226 Angle : 0.655 7.348 14366 Z= 0.342 Chirality : 0.046 0.162 1604 Planarity : 0.005 0.052 1882 Dihedral : 4.190 16.923 1404 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.18 % Allowed : 0.62 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.32 (0.22), residues: 1310 helix: 0.63 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -0.40 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 117 HIS 0.005 0.001 HIS A 62 PHE 0.012 0.002 PHE E 168 TYR 0.019 0.002 TYR F 130 ARG 0.010 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 398 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.7379 (mmp) cc_final: 0.6851 (tpp) REVERT: A 29 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7929 (mt-10) REVERT: A 30 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7858 (tptm) REVERT: A 40 PHE cc_start: 0.9092 (t80) cc_final: 0.8641 (t80) REVERT: A 53 ASN cc_start: 0.8747 (m-40) cc_final: 0.8377 (m110) REVERT: A 68 MET cc_start: 0.9360 (ppp) cc_final: 0.8964 (ppp) REVERT: A 71 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8683 (mt-10) REVERT: A 100 ARG cc_start: 0.8831 (ttt180) cc_final: 0.8257 (tmm-80) REVERT: A 103 ASP cc_start: 0.9185 (m-30) cc_final: 0.8280 (m-30) REVERT: A 132 ARG cc_start: 0.9304 (tmt-80) cc_final: 0.8907 (tpt90) REVERT: A 136 LEU cc_start: 0.9485 (tt) cc_final: 0.9089 (tt) REVERT: A 139 ASN cc_start: 0.8789 (t0) cc_final: 0.8545 (t0) REVERT: A 149 SER cc_start: 0.9327 (t) cc_final: 0.8931 (p) REVERT: A 152 ASP cc_start: 0.9186 (m-30) cc_final: 0.8828 (m-30) REVERT: A 192 GLN cc_start: 0.9390 (mp10) cc_final: 0.9113 (mp10) REVERT: A 203 LYS cc_start: 0.9330 (mttt) cc_final: 0.9016 (mttt) REVERT: A 214 MET cc_start: 0.8860 (mmp) cc_final: 0.8617 (mmt) REVERT: B 28 GLU cc_start: 0.8989 (pt0) cc_final: 0.8749 (pt0) REVERT: B 39 MET cc_start: 0.9587 (tpp) cc_final: 0.9131 (tmm) REVERT: B 51 ASP cc_start: 0.9125 (t0) cc_final: 0.8643 (t0) REVERT: B 55 MET cc_start: 0.9214 (mtm) cc_final: 0.8083 (mtm) REVERT: B 68 MET cc_start: 0.9093 (ttm) cc_final: 0.8680 (tpp) REVERT: B 96 MET cc_start: 0.9160 (mmp) cc_final: 0.8800 (mpp) REVERT: B 103 ASP cc_start: 0.9292 (m-30) cc_final: 0.8960 (m-30) REVERT: B 112 GLN cc_start: 0.9758 (tp40) cc_final: 0.9402 (tp-100) REVERT: B 170 LYS cc_start: 0.9058 (pttt) cc_final: 0.8854 (pttm) REVERT: B 215 MET cc_start: 0.8804 (mtm) cc_final: 0.8534 (mtm) REVERT: C 52 LEU cc_start: 0.9686 (mp) cc_final: 0.9423 (mp) REVERT: C 68 MET cc_start: 0.9359 (mtp) cc_final: 0.8948 (mtt) REVERT: C 103 ASP cc_start: 0.9053 (m-30) cc_final: 0.8537 (m-30) REVERT: C 104 ILE cc_start: 0.8844 (tt) cc_final: 0.8419 (pt) REVERT: C 128 GLU cc_start: 0.9523 (mp0) cc_final: 0.9248 (mp0) REVERT: C 158 LYS cc_start: 0.9192 (mmmt) cc_final: 0.8827 (mmmm) REVERT: C 168 PHE cc_start: 0.9508 (t80) cc_final: 0.9105 (t80) REVERT: C 190 LEU cc_start: 0.9390 (mt) cc_final: 0.9141 (mt) REVERT: D 23 TRP cc_start: 0.9120 (t-100) cc_final: 0.8852 (t-100) REVERT: D 29 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7865 (mt-10) REVERT: D 53 ASN cc_start: 0.8659 (m-40) cc_final: 0.8252 (m110) REVERT: D 96 MET cc_start: 0.1212 (mmt) cc_final: 0.0884 (mpp) REVERT: D 100 ARG cc_start: 0.8925 (ttt180) cc_final: 0.8645 (tmm-80) REVERT: D 129 ILE cc_start: 0.9101 (mt) cc_final: 0.8720 (tt) REVERT: D 132 ARG cc_start: 0.9300 (tmt-80) cc_final: 0.8895 (tpt90) REVERT: D 136 LEU cc_start: 0.9605 (tt) cc_final: 0.9284 (tt) REVERT: D 161 PHE cc_start: 0.8211 (t80) cc_final: 0.7942 (t80) REVERT: D 168 PHE cc_start: 0.9187 (t80) cc_final: 0.8923 (t80) REVERT: D 169 TYR cc_start: 0.9249 (m-80) cc_final: 0.8893 (m-80) REVERT: D 170 LYS cc_start: 0.9068 (pttm) cc_final: 0.8813 (pttm) REVERT: D 203 LYS cc_start: 0.9404 (mttt) cc_final: 0.9173 (mttt) REVERT: D 212 GLU cc_start: 0.9023 (pt0) cc_final: 0.8508 (pm20) REVERT: E 35 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8283 (tm-30) REVERT: E 68 MET cc_start: 0.8806 (mtp) cc_final: 0.8453 (tpp) REVERT: E 84 HIS cc_start: 0.9440 (m90) cc_final: 0.8794 (t-90) REVERT: E 96 MET cc_start: 0.8588 (mmp) cc_final: 0.7571 (mpp) REVERT: E 124 ILE cc_start: 0.8207 (mm) cc_final: 0.7748 (mm) REVERT: E 140 LYS cc_start: 0.9490 (mttt) cc_final: 0.9120 (tttt) REVERT: E 141 ILE cc_start: 0.9289 (mt) cc_final: 0.8986 (mt) REVERT: E 144 MET cc_start: 0.8624 (ppp) cc_final: 0.8152 (ppp) REVERT: E 170 LYS cc_start: 0.9191 (pttt) cc_final: 0.8699 (pttt) REVERT: E 215 MET cc_start: 0.8883 (mtm) cc_final: 0.8655 (ptp) REVERT: F 52 LEU cc_start: 0.9677 (mp) cc_final: 0.9465 (mp) REVERT: F 68 MET cc_start: 0.9302 (mtp) cc_final: 0.9042 (mtt) REVERT: F 104 ILE cc_start: 0.8996 (tt) cc_final: 0.8579 (pt) REVERT: F 118 MET cc_start: 0.8135 (mmp) cc_final: 0.7862 (mmm) REVERT: F 164 TYR cc_start: 0.8664 (t80) cc_final: 0.8224 (t80) REVERT: F 168 PHE cc_start: 0.9563 (t80) cc_final: 0.8984 (t80) REVERT: F 190 LEU cc_start: 0.9338 (mt) cc_final: 0.8940 (mt) REVERT: F 213 GLU cc_start: 0.9179 (pt0) cc_final: 0.8959 (pt0) outliers start: 2 outliers final: 0 residues processed: 400 average time/residue: 0.2545 time to fit residues: 136.4819 Evaluate side-chains 318 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 84 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.081668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.056703 restraints weight = 72327.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.059999 restraints weight = 39915.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.062398 restraints weight = 26801.666| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.7294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10566 Z= 0.266 Angle : 0.689 7.609 14366 Z= 0.364 Chirality : 0.047 0.197 1604 Planarity : 0.005 0.050 1882 Dihedral : 4.396 16.268 1404 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.18 % Allowed : 0.80 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.07 (0.22), residues: 1310 helix: 0.42 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -0.49 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 117 HIS 0.006 0.002 HIS A 62 PHE 0.020 0.003 PHE B 40 TYR 0.036 0.003 TYR D 145 ARG 0.008 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 393 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7947 (mt-10) REVERT: A 30 LYS cc_start: 0.8429 (mmtt) cc_final: 0.7985 (tptm) REVERT: A 40 PHE cc_start: 0.9126 (t80) cc_final: 0.8660 (t80) REVERT: A 53 ASN cc_start: 0.8784 (m-40) cc_final: 0.8426 (m110) REVERT: A 68 MET cc_start: 0.9346 (ppp) cc_final: 0.8964 (ppp) REVERT: A 71 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8717 (mt-10) REVERT: A 103 ASP cc_start: 0.9211 (m-30) cc_final: 0.8966 (m-30) REVERT: A 132 ARG cc_start: 0.9326 (tmt-80) cc_final: 0.8941 (tpt90) REVERT: A 136 LEU cc_start: 0.9490 (tt) cc_final: 0.9126 (tt) REVERT: A 139 ASN cc_start: 0.8855 (t0) cc_final: 0.8609 (t0) REVERT: A 149 SER cc_start: 0.9385 (t) cc_final: 0.9011 (p) REVERT: A 152 ASP cc_start: 0.9275 (m-30) cc_final: 0.8949 (m-30) REVERT: A 167 ARG cc_start: 0.9525 (mpp-170) cc_final: 0.9290 (mtm-85) REVERT: A 203 LYS cc_start: 0.9373 (mttt) cc_final: 0.9107 (mttt) REVERT: A 212 GLU cc_start: 0.9302 (pt0) cc_final: 0.8655 (pm20) REVERT: A 214 MET cc_start: 0.8936 (mmp) cc_final: 0.8679 (mmt) REVERT: B 28 GLU cc_start: 0.9045 (pt0) cc_final: 0.8818 (pt0) REVERT: B 39 MET cc_start: 0.9597 (tpp) cc_final: 0.9174 (tmm) REVERT: B 51 ASP cc_start: 0.9217 (t0) cc_final: 0.8742 (t0) REVERT: B 55 MET cc_start: 0.9216 (mtm) cc_final: 0.8077 (mtm) REVERT: B 68 MET cc_start: 0.9089 (ttm) cc_final: 0.8656 (tpp) REVERT: B 84 HIS cc_start: 0.9454 (m90) cc_final: 0.9203 (m-70) REVERT: B 96 MET cc_start: 0.9164 (mmp) cc_final: 0.8806 (mpp) REVERT: B 103 ASP cc_start: 0.9267 (m-30) cc_final: 0.9014 (m-30) REVERT: B 112 GLN cc_start: 0.9784 (tp40) cc_final: 0.9475 (tp-100) REVERT: B 118 MET cc_start: 0.8791 (mmt) cc_final: 0.8359 (ptp) REVERT: B 144 MET cc_start: 0.8615 (tmm) cc_final: 0.8381 (tmm) REVERT: B 215 MET cc_start: 0.8808 (mtm) cc_final: 0.8577 (mtm) REVERT: C 52 LEU cc_start: 0.9668 (mp) cc_final: 0.9457 (mp) REVERT: C 68 MET cc_start: 0.9361 (mtp) cc_final: 0.8973 (mtt) REVERT: C 103 ASP cc_start: 0.9063 (m-30) cc_final: 0.8564 (m-30) REVERT: C 128 GLU cc_start: 0.9573 (mp0) cc_final: 0.9285 (mp0) REVERT: C 152 ASP cc_start: 0.9127 (m-30) cc_final: 0.8857 (m-30) REVERT: C 158 LYS cc_start: 0.9215 (mmmt) cc_final: 0.8869 (mmmm) REVERT: C 168 PHE cc_start: 0.9526 (t80) cc_final: 0.9119 (t80) REVERT: C 190 LEU cc_start: 0.9403 (mt) cc_final: 0.9122 (mt) REVERT: D 29 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7901 (mt-10) REVERT: D 40 PHE cc_start: 0.9117 (t80) cc_final: 0.8636 (t80) REVERT: D 53 ASN cc_start: 0.8764 (m-40) cc_final: 0.8436 (m110) REVERT: D 96 MET cc_start: 0.1320 (mmt) cc_final: 0.1036 (mpp) REVERT: D 100 ARG cc_start: 0.8918 (ttt180) cc_final: 0.8355 (ttm-80) REVERT: D 128 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8128 (tm-30) REVERT: D 129 ILE cc_start: 0.9131 (mt) cc_final: 0.8737 (tt) REVERT: D 132 ARG cc_start: 0.9279 (tmt-80) cc_final: 0.8808 (tpt90) REVERT: D 136 LEU cc_start: 0.9592 (tt) cc_final: 0.9225 (tt) REVERT: D 161 PHE cc_start: 0.8394 (t80) cc_final: 0.8017 (t80) REVERT: D 169 TYR cc_start: 0.9324 (m-80) cc_final: 0.9049 (m-80) REVERT: D 170 LYS cc_start: 0.9067 (pttm) cc_final: 0.8659 (pttm) REVERT: D 203 LYS cc_start: 0.9508 (mttt) cc_final: 0.9206 (mttt) REVERT: D 212 GLU cc_start: 0.9009 (pt0) cc_final: 0.8549 (pm20) REVERT: D 214 MET cc_start: 0.8804 (mmp) cc_final: 0.8496 (mmm) REVERT: E 35 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8338 (tm-30) REVERT: E 68 MET cc_start: 0.8819 (mtp) cc_final: 0.8585 (tpp) REVERT: E 84 HIS cc_start: 0.9453 (m90) cc_final: 0.8880 (t70) REVERT: E 96 MET cc_start: 0.8707 (mmp) cc_final: 0.7832 (mpp) REVERT: E 140 LYS cc_start: 0.9484 (mttt) cc_final: 0.9092 (tttt) REVERT: E 141 ILE cc_start: 0.9336 (mt) cc_final: 0.9064 (mt) REVERT: E 144 MET cc_start: 0.8701 (ppp) cc_final: 0.8197 (ppp) REVERT: E 170 LYS cc_start: 0.9191 (pttt) cc_final: 0.8663 (pttt) REVERT: E 215 MET cc_start: 0.8977 (mtm) cc_final: 0.8667 (ptp) REVERT: F 52 LEU cc_start: 0.9658 (mp) cc_final: 0.9382 (mp) REVERT: F 68 MET cc_start: 0.9339 (mtp) cc_final: 0.9098 (mtt) REVERT: F 103 ASP cc_start: 0.8948 (m-30) cc_final: 0.8108 (t70) REVERT: F 104 ILE cc_start: 0.9013 (tt) cc_final: 0.8618 (pt) REVERT: F 118 MET cc_start: 0.8210 (mmp) cc_final: 0.7854 (mmm) REVERT: F 139 ASN cc_start: 0.9472 (t0) cc_final: 0.9250 (m-40) REVERT: F 140 LYS cc_start: 0.9458 (mtpp) cc_final: 0.9240 (mtpp) REVERT: F 164 TYR cc_start: 0.8731 (t80) cc_final: 0.7754 (t80) REVERT: F 167 ARG cc_start: 0.9436 (ptp90) cc_final: 0.8542 (ptp90) REVERT: F 168 PHE cc_start: 0.9555 (t80) cc_final: 0.9043 (t80) REVERT: F 185 MET cc_start: 0.8944 (mmp) cc_final: 0.8621 (mmm) REVERT: F 190 LEU cc_start: 0.9282 (mt) cc_final: 0.8967 (mt) REVERT: F 213 GLU cc_start: 0.9220 (pt0) cc_final: 0.9020 (pt0) REVERT: F 215 MET cc_start: 0.9456 (tmm) cc_final: 0.9231 (tmm) outliers start: 2 outliers final: 0 residues processed: 395 average time/residue: 0.2489 time to fit residues: 132.6343 Evaluate side-chains 310 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 81 optimal weight: 0.0570 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.082929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.055861 restraints weight = 99092.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.059567 restraints weight = 47414.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.062359 restraints weight = 30237.759| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.7502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10566 Z= 0.237 Angle : 0.680 9.983 14366 Z= 0.356 Chirality : 0.047 0.178 1604 Planarity : 0.005 0.057 1882 Dihedral : 4.415 15.459 1404 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.18 % Allowed : 0.27 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.06 (0.22), residues: 1310 helix: 0.40 (0.17), residues: 870 sheet: None (None), residues: 0 loop : -0.45 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 117 HIS 0.005 0.001 HIS A 62 PHE 0.010 0.002 PHE B 40 TYR 0.020 0.002 TYR B 169 ARG 0.017 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 390 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7890 (mt-10) REVERT: A 30 LYS cc_start: 0.8313 (mmtt) cc_final: 0.7908 (tptm) REVERT: A 40 PHE cc_start: 0.9104 (t80) cc_final: 0.8584 (t80) REVERT: A 53 ASN cc_start: 0.8787 (m-40) cc_final: 0.8478 (m110) REVERT: A 100 ARG cc_start: 0.8984 (ttt180) cc_final: 0.8444 (tmm-80) REVERT: A 103 ASP cc_start: 0.9261 (m-30) cc_final: 0.8385 (m-30) REVERT: A 131 LYS cc_start: 0.9295 (pttt) cc_final: 0.9057 (ptmt) REVERT: A 132 ARG cc_start: 0.9332 (tmt-80) cc_final: 0.8922 (tpt90) REVERT: A 136 LEU cc_start: 0.9516 (tt) cc_final: 0.9163 (tt) REVERT: A 139 ASN cc_start: 0.8900 (t0) cc_final: 0.8657 (t0) REVERT: A 149 SER cc_start: 0.9383 (t) cc_final: 0.9072 (p) REVERT: A 152 ASP cc_start: 0.9330 (m-30) cc_final: 0.9039 (m-30) REVERT: A 167 ARG cc_start: 0.9550 (mpp-170) cc_final: 0.9180 (mtm-85) REVERT: A 168 PHE cc_start: 0.9018 (t80) cc_final: 0.8797 (t80) REVERT: A 192 GLN cc_start: 0.9377 (mp10) cc_final: 0.9157 (mp10) REVERT: A 203 LYS cc_start: 0.9366 (mttt) cc_final: 0.9048 (mttt) REVERT: A 212 GLU cc_start: 0.9247 (pt0) cc_final: 0.8642 (pm20) REVERT: B 39 MET cc_start: 0.9609 (tpp) cc_final: 0.9125 (tmm) REVERT: B 68 MET cc_start: 0.9106 (ttm) cc_final: 0.8683 (tpp) REVERT: B 84 HIS cc_start: 0.9442 (m90) cc_final: 0.9190 (m-70) REVERT: B 96 MET cc_start: 0.9195 (mmp) cc_final: 0.8826 (mpp) REVERT: B 103 ASP cc_start: 0.9323 (m-30) cc_final: 0.9016 (m-30) REVERT: B 112 GLN cc_start: 0.9783 (tp40) cc_final: 0.9497 (tp-100) REVERT: B 144 MET cc_start: 0.8633 (tmm) cc_final: 0.8416 (tmm) REVERT: B 215 MET cc_start: 0.8881 (mtm) cc_final: 0.8598 (mtm) REVERT: C 52 LEU cc_start: 0.9656 (mp) cc_final: 0.9412 (mp) REVERT: C 68 MET cc_start: 0.9379 (mtp) cc_final: 0.9053 (mtt) REVERT: C 103 ASP cc_start: 0.8985 (m-30) cc_final: 0.8242 (t70) REVERT: C 128 GLU cc_start: 0.9523 (mp0) cc_final: 0.9217 (mp0) REVERT: C 140 LYS cc_start: 0.9352 (mttm) cc_final: 0.9131 (ttmm) REVERT: C 158 LYS cc_start: 0.9231 (mmmt) cc_final: 0.8874 (mmmm) REVERT: C 168 PHE cc_start: 0.9529 (t80) cc_final: 0.8992 (t80) REVERT: C 190 LEU cc_start: 0.9404 (mt) cc_final: 0.9098 (mt) REVERT: D 29 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7748 (mt-10) REVERT: D 53 ASN cc_start: 0.8756 (m-40) cc_final: 0.8395 (m110) REVERT: D 100 ARG cc_start: 0.8888 (ttt180) cc_final: 0.8320 (ttm-80) REVERT: D 129 ILE cc_start: 0.9146 (mt) cc_final: 0.8881 (tt) REVERT: D 132 ARG cc_start: 0.9309 (tmt-80) cc_final: 0.8898 (tpt90) REVERT: D 136 LEU cc_start: 0.9611 (tt) cc_final: 0.9279 (tt) REVERT: D 145 TYR cc_start: 0.8270 (m-80) cc_final: 0.7387 (m-80) REVERT: D 164 TYR cc_start: 0.8634 (t80) cc_final: 0.8146 (t80) REVERT: D 168 PHE cc_start: 0.9099 (t80) cc_final: 0.8803 (t80) REVERT: D 203 LYS cc_start: 0.9439 (mttt) cc_final: 0.9202 (mttt) REVERT: D 212 GLU cc_start: 0.8921 (pt0) cc_final: 0.8583 (pm20) REVERT: E 35 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8345 (tm-30) REVERT: E 68 MET cc_start: 0.8864 (mtp) cc_final: 0.8053 (tpp) REVERT: E 71 GLU cc_start: 0.8364 (pp20) cc_final: 0.8162 (pp20) REVERT: E 96 MET cc_start: 0.8809 (mmp) cc_final: 0.8023 (mpp) REVERT: E 140 LYS cc_start: 0.9471 (mttt) cc_final: 0.9071 (tttt) REVERT: E 144 MET cc_start: 0.8673 (ppp) cc_final: 0.8229 (ppp) REVERT: E 215 MET cc_start: 0.8993 (mtm) cc_final: 0.8609 (ptp) REVERT: F 52 LEU cc_start: 0.9653 (mp) cc_final: 0.9378 (mp) REVERT: F 103 ASP cc_start: 0.8833 (m-30) cc_final: 0.8134 (t70) REVERT: F 104 ILE cc_start: 0.9034 (tt) cc_final: 0.8658 (pt) REVERT: F 118 MET cc_start: 0.8225 (mmp) cc_final: 0.7833 (mmm) REVERT: F 132 ARG cc_start: 0.9388 (mtt180) cc_final: 0.9036 (mtt180) REVERT: F 149 SER cc_start: 0.8969 (t) cc_final: 0.8343 (p) REVERT: F 152 ASP cc_start: 0.9479 (m-30) cc_final: 0.9260 (m-30) REVERT: F 159 GLU cc_start: 0.8611 (pt0) cc_final: 0.7835 (mp0) REVERT: F 164 TYR cc_start: 0.8634 (t80) cc_final: 0.7701 (t80) REVERT: F 167 ARG cc_start: 0.9416 (ptp90) cc_final: 0.8550 (ptp90) REVERT: F 168 PHE cc_start: 0.9527 (t80) cc_final: 0.8929 (t80) REVERT: F 185 MET cc_start: 0.8935 (mmp) cc_final: 0.8610 (mmm) REVERT: F 190 LEU cc_start: 0.9123 (mt) cc_final: 0.8906 (mt) outliers start: 2 outliers final: 0 residues processed: 392 average time/residue: 0.2483 time to fit residues: 130.9644 Evaluate side-chains 311 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 122 optimal weight: 0.4980 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 34 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 95 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.082611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.057930 restraints weight = 66331.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.061147 restraints weight = 37782.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.063488 restraints weight = 25698.174| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.7606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10566 Z= 0.221 Angle : 0.688 8.845 14366 Z= 0.358 Chirality : 0.046 0.185 1604 Planarity : 0.005 0.055 1882 Dihedral : 4.416 14.635 1404 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.11 (0.22), residues: 1310 helix: 0.39 (0.17), residues: 862 sheet: None (None), residues: 0 loop : -0.33 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 117 HIS 0.005 0.001 HIS A 62 PHE 0.027 0.002 PHE B 40 TYR 0.017 0.002 TYR B 169 ARG 0.013 0.001 ARG A 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 393 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7817 (mt-10) REVERT: A 30 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7912 (tptm) REVERT: A 53 ASN cc_start: 0.8820 (m-40) cc_final: 0.8456 (m110) REVERT: A 68 MET cc_start: 0.9311 (ppp) cc_final: 0.8828 (ppp) REVERT: A 71 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8682 (mt-10) REVERT: A 100 ARG cc_start: 0.8966 (ttt180) cc_final: 0.8420 (tmm-80) REVERT: A 103 ASP cc_start: 0.9126 (m-30) cc_final: 0.8271 (m-30) REVERT: A 131 LYS cc_start: 0.9298 (pttt) cc_final: 0.9054 (ptmt) REVERT: A 132 ARG cc_start: 0.9331 (tmt-80) cc_final: 0.8953 (tpt90) REVERT: A 136 LEU cc_start: 0.9506 (tt) cc_final: 0.9205 (tt) REVERT: A 140 LYS cc_start: 0.9546 (ttmt) cc_final: 0.9299 (tmtt) REVERT: A 141 ILE cc_start: 0.9355 (mt) cc_final: 0.9030 (mt) REVERT: A 149 SER cc_start: 0.9370 (t) cc_final: 0.8990 (p) REVERT: A 152 ASP cc_start: 0.9282 (m-30) cc_final: 0.9016 (m-30) REVERT: A 168 PHE cc_start: 0.8963 (t80) cc_final: 0.8674 (t80) REVERT: A 192 GLN cc_start: 0.9338 (mp10) cc_final: 0.9137 (mp10) REVERT: A 203 LYS cc_start: 0.9356 (mttt) cc_final: 0.9043 (mttt) REVERT: A 212 GLU cc_start: 0.9254 (pt0) cc_final: 0.8866 (pm20) REVERT: A 215 MET cc_start: 0.8842 (ptm) cc_final: 0.8598 (ppp) REVERT: B 39 MET cc_start: 0.9591 (tpp) cc_final: 0.9091 (tmm) REVERT: B 55 MET cc_start: 0.9532 (ttp) cc_final: 0.9096 (tmm) REVERT: B 68 MET cc_start: 0.9000 (ttm) cc_final: 0.8525 (tpp) REVERT: B 84 HIS cc_start: 0.9407 (m90) cc_final: 0.9158 (m-70) REVERT: B 96 MET cc_start: 0.9154 (mmp) cc_final: 0.8847 (mpp) REVERT: B 103 ASP cc_start: 0.9275 (m-30) cc_final: 0.8972 (m-30) REVERT: B 112 GLN cc_start: 0.9758 (tp40) cc_final: 0.9472 (tp-100) REVERT: B 144 MET cc_start: 0.8560 (tmm) cc_final: 0.8319 (tmm) REVERT: B 170 LYS cc_start: 0.9569 (tmtt) cc_final: 0.9217 (pttm) REVERT: C 52 LEU cc_start: 0.9688 (mp) cc_final: 0.9435 (mp) REVERT: C 68 MET cc_start: 0.9405 (mtp) cc_final: 0.9092 (mtt) REVERT: C 103 ASP cc_start: 0.8853 (m-30) cc_final: 0.8005 (t70) REVERT: C 104 ILE cc_start: 0.8795 (tt) cc_final: 0.8290 (pt) REVERT: C 128 GLU cc_start: 0.9495 (mp0) cc_final: 0.9247 (mp0) REVERT: C 140 LYS cc_start: 0.9383 (mttm) cc_final: 0.9159 (ttmm) REVERT: C 158 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8847 (mmmm) REVERT: C 168 PHE cc_start: 0.9494 (t80) cc_final: 0.8974 (t80) REVERT: C 190 LEU cc_start: 0.9373 (mt) cc_final: 0.9162 (mt) REVERT: C 215 MET cc_start: 0.9253 (tmm) cc_final: 0.9045 (tmm) REVERT: D 29 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7690 (mt-10) REVERT: D 53 ASN cc_start: 0.8596 (m-40) cc_final: 0.8209 (m110) REVERT: D 71 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8848 (mt-10) REVERT: D 100 ARG cc_start: 0.8861 (ttt180) cc_final: 0.8101 (ttm-80) REVERT: D 132 ARG cc_start: 0.9223 (tmt-80) cc_final: 0.8833 (tpt90) REVERT: D 136 LEU cc_start: 0.9592 (tt) cc_final: 0.9291 (tt) REVERT: D 145 TYR cc_start: 0.7796 (m-80) cc_final: 0.7402 (m-80) REVERT: D 164 TYR cc_start: 0.8596 (t80) cc_final: 0.8078 (t80) REVERT: D 168 PHE cc_start: 0.9108 (t80) cc_final: 0.8826 (t80) REVERT: D 203 LYS cc_start: 0.9525 (mttt) cc_final: 0.9190 (mttt) REVERT: D 212 GLU cc_start: 0.8937 (pt0) cc_final: 0.8592 (pm20) REVERT: D 214 MET cc_start: 0.8822 (mmp) cc_final: 0.8459 (mmm) REVERT: E 35 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8362 (tm-30) REVERT: E 68 MET cc_start: 0.8775 (mtp) cc_final: 0.8354 (tpp) REVERT: E 84 HIS cc_start: 0.9489 (m90) cc_final: 0.8927 (t70) REVERT: E 96 MET cc_start: 0.8830 (mmp) cc_final: 0.8282 (mpp) REVERT: E 132 ARG cc_start: 0.8810 (ptp90) cc_final: 0.8544 (ptp-170) REVERT: E 140 LYS cc_start: 0.9445 (mttt) cc_final: 0.9061 (tttt) REVERT: E 141 ILE cc_start: 0.9377 (mt) cc_final: 0.9081 (mt) REVERT: E 144 MET cc_start: 0.8576 (ppp) cc_final: 0.8122 (ppp) REVERT: E 170 LYS cc_start: 0.9112 (pttt) cc_final: 0.8630 (pttt) REVERT: E 215 MET cc_start: 0.9008 (mtm) cc_final: 0.8593 (ptp) REVERT: F 52 LEU cc_start: 0.9651 (mp) cc_final: 0.9374 (mp) REVERT: F 103 ASP cc_start: 0.8782 (m-30) cc_final: 0.8253 (t70) REVERT: F 104 ILE cc_start: 0.9061 (tt) cc_final: 0.8646 (pt) REVERT: F 118 MET cc_start: 0.8242 (mmp) cc_final: 0.7925 (mmm) REVERT: F 132 ARG cc_start: 0.9363 (mtt180) cc_final: 0.8989 (mtt180) REVERT: F 149 SER cc_start: 0.8951 (t) cc_final: 0.8299 (p) REVERT: F 152 ASP cc_start: 0.9438 (m-30) cc_final: 0.9232 (m-30) REVERT: F 159 GLU cc_start: 0.8594 (pt0) cc_final: 0.7853 (mp0) REVERT: F 164 TYR cc_start: 0.8622 (t80) cc_final: 0.8139 (t80) REVERT: F 168 PHE cc_start: 0.9540 (t80) cc_final: 0.8932 (t80) REVERT: F 185 MET cc_start: 0.8834 (mmp) cc_final: 0.8524 (mmm) REVERT: F 190 LEU cc_start: 0.9120 (mt) cc_final: 0.8762 (mt) outliers start: 2 outliers final: 0 residues processed: 395 average time/residue: 0.2450 time to fit residues: 130.4712 Evaluate side-chains 310 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.080398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.056348 restraints weight = 59911.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.059238 restraints weight = 35711.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.061421 restraints weight = 25085.135| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.7842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10566 Z= 0.285 Angle : 0.732 8.536 14366 Z= 0.389 Chirality : 0.048 0.182 1604 Planarity : 0.005 0.050 1882 Dihedral : 4.575 20.635 1404 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.09 % Allowed : 0.53 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.22), residues: 1310 helix: 0.16 (0.17), residues: 870 sheet: None (None), residues: 0 loop : -0.41 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP D 23 HIS 0.007 0.002 HIS A 62 PHE 0.011 0.002 PHE A 40 TYR 0.035 0.003 TYR D 130 ARG 0.011 0.001 ARG A 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3795.88 seconds wall clock time: 68 minutes 36.68 seconds (4116.68 seconds total)