Starting phenix.real_space_refine on Mon Jul 28 05:08:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6skm_10228/07_2025/6skm_10228.cif Found real_map, /net/cci-nas-00/data/ceres_data/6skm_10228/07_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_10228/07_2025/6skm_10228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6skm_10228/07_2025/6skm_10228.map" model { file = "/net/cci-nas-00/data/ceres_data/6skm_10228/07_2025/6skm_10228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6skm_10228/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.80, per 1000 atoms: 0.75 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: 2.49 Conformation dependent library (CDL) restraints added in 1.8 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: 0.84 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: 2.68 Time building geometry restraints manager: 2.99 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: 0.130 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.670 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.850 ------------------------------------------------------------------------------- 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 : 0.006 0.505 10572 Z= 0.358 Angle : 0.753 44.143 14378 Z= 0.462 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 Details of bonding type rmsd hydrogen bonds : bond 0.13360 ( 577) hydrogen bonds : angle 4.66128 ( 1731) SS BOND : bond 0.21559 ( 6) SS BOND : angle 13.84335 ( 12) covalent geometry : bond 0.00350 (10566) covalent geometry : angle 0.63811 (14366) *********************** 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 : 1.215 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: 0.2783 time to fit residues: 226.8817 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 : 1.266 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.064429 restraints weight = 76759.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.068122 restraints weight = 41699.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.070845 restraints weight = 27813.953| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- 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 10572 Z= 0.173 Angle : 0.663 7.556 14378 Z= 0.344 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 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 577) hydrogen bonds : angle 3.84986 ( 1731) SS BOND : bond 0.00511 ( 6) SS BOND : angle 2.52313 ( 12) covalent geometry : bond 0.00390 (10566) covalent geometry : angle 0.65976 (14366) *********************** 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 : 1.196 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: 0.6927 (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: 0.9098 (t80) cc_final: 0.8590 (t80) REVERT: A 53 ASN cc_start: 0.8548 (m-40) cc_final: 0.8295 (m-40) REVERT: A 55 MET cc_start: 0.8659 (mtp) cc_final: 0.8302 (mtp) REVERT: A 71 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8574 (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: 0.8522 (pp30) REVERT: A 126 VAL cc_start: 0.6048 (t) cc_final: 0.5475 (p) REVERT: A 128 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 129 ILE cc_start: 0.8876 (mt) cc_final: 0.8515 (tt) REVERT: A 136 LEU cc_start: 0.9557 (tt) cc_final: 0.8903 (tt) REVERT: A 141 ILE cc_start: 0.9426 (mt) cc_final: 0.9080 (mt) REVERT: A 149 SER cc_start: 0.9019 (t) cc_final: 0.8675 (p) REVERT: A 168 PHE cc_start: 0.9073 (t80) cc_final: 0.8867 (t80) REVERT: A 190 LEU cc_start: 0.8548 (tp) cc_final: 0.8255 (tp) REVERT: A 212 GLU cc_start: 0.9087 (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: 0.9075 (t0) cc_final: 0.8851 (t0) REVERT: B 55 MET cc_start: 0.8759 (mtm) cc_final: 0.8332 (mtm) REVERT: B 68 MET cc_start: 0.9031 (mtp) cc_final: 0.8796 (mtp) REVERT: B 96 MET cc_start: 0.8741 (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: 0.9333 (mp0) REVERT: B 135 ILE cc_start: 0.9283 (pt) cc_final: 0.8980 (pt) REVERT: B 170 LYS cc_start: 0.9368 (pttm) cc_final: 0.9105 (pttp) REVERT: B 182 LYS cc_start: 0.9450 (ptpt) cc_final: 0.9235 (ptpt) REVERT: B 215 MET cc_start: 0.8874 (mtm) cc_final: 0.8632 (ptp) REVERT: C 5 ASN cc_start: 0.8137 (t0) cc_final: 0.7188 (p0) REVERT: C 68 MET cc_start: 0.9418 (mtp) cc_final: 0.8914 (mtt) REVERT: C 103 ASP cc_start: 0.9212 (m-30) cc_final: 0.8170 (t0) REVERT: C 104 ILE cc_start: 0.8687 (tt) cc_final: 0.8098 (pt) REVERT: C 112 GLN cc_start: 0.9644 (tm-30) cc_final: 0.9438 (tm-30) REVERT: C 113 GLU cc_start: 0.9391 (mt-10) cc_final: 0.8138 (mm-30) REVERT: C 158 LYS cc_start: 0.9197 (mmmt) cc_final: 0.8849 (mmmm) REVERT: C 168 PHE cc_start: 0.9509 (t80) cc_final: 0.9228 (t80) REVERT: D 10 MET cc_start: 0.6538 (mmp) cc_final: 0.5962 (tpp) REVERT: D 40 PHE cc_start: 0.9039 (t80) cc_final: 0.8672 (t80) REVERT: D 53 ASN cc_start: 0.8399 (m-40) cc_final: 0.8119 (m110) REVERT: D 55 MET cc_start: 0.9636 (ttm) cc_final: 0.9387 (ttt) REVERT: D 100 ARG cc_start: 0.9069 (ttt180) cc_final: 0.8332 (tmm-80) REVERT: D 103 ASP cc_start: 0.9077 (m-30) cc_final: 0.8169 (m-30) REVERT: D 126 VAL cc_start: 0.6818 (t) cc_final: 0.6618 (p) REVERT: D 128 GLU cc_start: 0.8438 (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: 0.8267 (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: 0.8989 (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: 0.9315 (m90) cc_final: 0.8721 (t-90) REVERT: E 96 MET cc_start: 0.8345 (mmp) cc_final: 0.7834 (mmp) REVERT: E 115 ILE cc_start: 0.9791 (mm) cc_final: 0.9352 (mm) REVERT: E 140 LYS cc_start: 0.9283 (mttt) cc_final: 0.8973 (mtpt) REVERT: E 141 ILE cc_start: 0.9007 (mt) cc_final: 0.8665 (mt) REVERT: E 144 MET cc_start: 0.8428 (ppp) cc_final: 0.8143 (ppp) REVERT: E 211 LEU cc_start: 0.9349 (tt) cc_final: 0.8991 (tt) REVERT: E 215 MET cc_start: 0.8989 (mmp) cc_final: 0.8709 (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: 0.9075 (m-30) cc_final: 0.7960 (t0) REVERT: F 104 ILE cc_start: 0.8664 (tt) cc_final: 0.8356 (pt) REVERT: F 118 MET cc_start: 0.7625 (mmp) cc_final: 0.7351 (mmp) REVERT: F 164 TYR cc_start: 0.8548 (t80) cc_final: 0.7712 (t80) REVERT: F 167 ARG cc_start: 0.9203 (ptp90) cc_final: 0.8381 (ptp90) REVERT: F 168 PHE cc_start: 0.9363 (t80) cc_final: 0.9009 (t80) REVERT: F 185 MET cc_start: 0.8850 (mmp) cc_final: 0.8557 (mmm) REVERT: F 190 LEU cc_start: 0.9404 (mt) cc_final: 0.8814 (mt) outliers start: 1 outliers final: 0 residues processed: 486 average time/residue: 0.2915 time to fit residues: 190.0447 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 : 1.366 ------------------------------------------------------------------------------- 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: 10.0000 chunk 19 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.060341 restraints weight = 82032.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.063982 restraints weight = 43562.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.066676 restraints weight = 28840.471| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 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 = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10572 Z= 0.179 Angle : 0.654 6.634 14378 Z= 0.341 Chirality : 0.045 0.248 1604 Planarity : 0.005 0.048 1882 Dihedral : 3.781 19.628 1404 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.18 % Allowed : 2.74 % Favored : 97.08 % 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: 0.28 (0.22), residues: 1310 helix: 0.73 (0.17), residues: 838 sheet: None (None), residues: 0 loop : -0.67 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 80 HIS 0.005 0.001 HIS B 84 PHE 0.032 0.003 PHE C 161 TYR 0.015 0.002 TYR B 169 ARG 0.006 0.001 ARG F 154 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 577) hydrogen bonds : angle 3.93491 ( 1731) SS BOND : bond 0.00590 ( 6) SS BOND : angle 1.43442 ( 12) covalent geometry : bond 0.00388 (10566) covalent geometry : angle 0.65253 (14366) *********************** 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 : 2.036 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: A 10 MET cc_start: 0.7104 (mmp) cc_final: 0.6304 (tpp) REVERT: A 29 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8064 (pt0) REVERT: A 30 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7732 (tptm) REVERT: A 40 PHE cc_start: 0.9137 (t80) cc_final: 0.8641 (t80) REVERT: A 53 ASN cc_start: 0.8640 (m-40) cc_final: 0.8266 (m110) REVERT: A 68 MET cc_start: 0.9325 (ppp) cc_final: 0.8916 (ppp) REVERT: A 71 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8454 (mt-10) REVERT: A 87 HIS cc_start: 0.8266 (m-70) cc_final: 0.7732 (t70) REVERT: A 113 GLU cc_start: 0.9319 (mt-10) cc_final: 0.9059 (tt0) REVERT: A 114 GLN cc_start: 0.8886 (pp30) cc_final: 0.8622 (pp30) REVERT: A 132 ARG cc_start: 0.9282 (tmt-80) cc_final: 0.8875 (tpt90) REVERT: A 136 LEU cc_start: 0.9499 (tt) cc_final: 0.9035 (tt) REVERT: A 139 ASN cc_start: 0.8897 (t0) cc_final: 0.8672 (t0) REVERT: A 149 SER cc_start: 0.9066 (t) cc_final: 0.8577 (p) REVERT: A 152 ASP cc_start: 0.9015 (m-30) cc_final: 0.8744 (m-30) REVERT: A 164 TYR cc_start: 0.8297 (t80) cc_final: 0.8026 (t80) REVERT: A 203 LYS cc_start: 0.9276 (mttt) cc_final: 0.8939 (mttt) REVERT: A 212 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8374 (pm20) REVERT: B 39 MET cc_start: 0.9552 (tpp) cc_final: 0.8941 (tpt) REVERT: B 51 ASP cc_start: 0.9165 (t0) cc_final: 0.8725 (t0) REVERT: B 55 MET cc_start: 0.8882 (mtm) cc_final: 0.8159 (mtm) REVERT: B 68 MET cc_start: 0.9070 (mtp) cc_final: 0.8783 (mtp) REVERT: B 84 HIS cc_start: 0.9386 (m90) cc_final: 0.8630 (t-90) REVERT: B 96 MET cc_start: 0.8863 (mmp) cc_final: 0.8235 (mpp) REVERT: B 103 ASP cc_start: 0.9215 (m-30) cc_final: 0.8804 (m-30) REVERT: B 112 GLN cc_start: 0.9759 (tp40) cc_final: 0.9469 (tp-100) REVERT: B 135 ILE cc_start: 0.9359 (pt) cc_final: 0.9130 (pt) REVERT: C 52 LEU cc_start: 0.9600 (mp) cc_final: 0.9372 (mp) REVERT: C 68 MET cc_start: 0.9345 (mtp) cc_final: 0.9065 (mtt) REVERT: C 103 ASP cc_start: 0.9151 (m-30) cc_final: 0.7847 (t0) REVERT: C 104 ILE cc_start: 0.8550 (tt) cc_final: 0.8102 (pt) REVERT: C 113 GLU cc_start: 0.9464 (mt-10) cc_final: 0.9028 (tt0) REVERT: C 158 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8841 (mmmm) REVERT: C 167 ARG cc_start: 0.9427 (ptp90) cc_final: 0.8542 (ptp90) REVERT: C 168 PHE cc_start: 0.9491 (t80) cc_final: 0.9243 (t80) REVERT: D 23 TRP cc_start: 0.8882 (t-100) cc_final: 0.8584 (t-100) REVERT: D 40 PHE cc_start: 0.9156 (t80) cc_final: 0.8600 (t80) REVERT: D 53 ASN cc_start: 0.8544 (m-40) cc_final: 0.8231 (m110) REVERT: D 100 ARG cc_start: 0.8876 (ttt180) cc_final: 0.8610 (tmm-80) REVERT: D 114 GLN cc_start: 0.9487 (pt0) cc_final: 0.9216 (pp30) REVERT: D 118 MET cc_start: 0.8998 (ptp) cc_final: 0.8745 (mmm) REVERT: D 128 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7904 (tm-30) REVERT: D 129 ILE cc_start: 0.9107 (mt) cc_final: 0.8753 (tt) REVERT: D 131 LYS cc_start: 0.9496 (tttt) cc_final: 0.9261 (ptpt) REVERT: D 144 MET cc_start: 0.9351 (ttt) cc_final: 0.8980 (ttt) REVERT: D 164 TYR cc_start: 0.8335 (t80) cc_final: 0.8049 (t80) REVERT: D 168 PHE cc_start: 0.9104 (t80) cc_final: 0.8902 (t80) REVERT: D 212 GLU cc_start: 0.9144 (pt0) cc_final: 0.8553 (pm20) REVERT: E 28 GLU cc_start: 0.9023 (pt0) cc_final: 0.8601 (pp20) REVERT: E 35 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8043 (tm-30) REVERT: E 68 MET cc_start: 0.8889 (mtp) cc_final: 0.8563 (tpp) REVERT: E 84 HIS cc_start: 0.9476 (m90) cc_final: 0.8827 (t-90) REVERT: E 96 MET cc_start: 0.8422 (mmp) cc_final: 0.7810 (mpp) REVERT: E 103 ASP cc_start: 0.8940 (m-30) cc_final: 0.8522 (m-30) REVERT: E 124 ILE cc_start: 0.8615 (mp) cc_final: 0.7716 (mp) REVERT: E 140 LYS cc_start: 0.9345 (mttt) cc_final: 0.9054 (mtpt) REVERT: E 141 ILE cc_start: 0.9129 (mt) cc_final: 0.8777 (mt) REVERT: E 144 MET cc_start: 0.8543 (ppp) cc_final: 0.8100 (ppp) REVERT: E 145 TYR cc_start: 0.8391 (t80) cc_final: 0.8154 (t80) REVERT: F 52 LEU cc_start: 0.9831 (mp) cc_final: 0.9595 (mp) REVERT: F 68 MET cc_start: 0.9406 (mtp) cc_final: 0.9119 (mtt) REVERT: F 103 ASP cc_start: 0.9079 (m-30) cc_final: 0.8079 (t70) REVERT: F 104 ILE cc_start: 0.8831 (tt) cc_final: 0.8477 (pt) REVERT: F 139 ASN cc_start: 0.9536 (t0) cc_final: 0.9307 (m-40) REVERT: F 140 LYS cc_start: 0.9445 (mtpp) cc_final: 0.9223 (mtpp) REVERT: F 164 TYR cc_start: 0.8704 (t80) cc_final: 0.7766 (t80) REVERT: F 167 ARG cc_start: 0.9282 (ptp90) cc_final: 0.8478 (ptp90) REVERT: F 168 PHE cc_start: 0.9491 (t80) cc_final: 0.9102 (t80) REVERT: F 190 LEU cc_start: 0.9481 (mt) cc_final: 0.8823 (mt) outliers start: 2 outliers final: 0 residues processed: 443 average time/residue: 0.3557 time to fit residues: 212.7924 Evaluate side-chains 330 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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: 0.6980 chunk 62 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.087526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.060991 restraints weight = 68164.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.064396 restraints weight = 38861.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.066927 restraints weight = 26451.400| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10572 Z= 0.147 Angle : 0.631 6.450 14378 Z= 0.330 Chirality : 0.046 0.162 1604 Planarity : 0.005 0.041 1882 Dihedral : 4.006 21.478 1404 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.60 % Favored : 97.32 % 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: 0.35 (0.22), residues: 1310 helix: 0.76 (0.17), residues: 848 sheet: None (None), residues: 0 loop : -0.62 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 80 HIS 0.005 0.001 HIS D 62 PHE 0.026 0.002 PHE C 161 TYR 0.012 0.002 TYR B 169 ARG 0.014 0.001 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 577) hydrogen bonds : angle 3.95662 ( 1731) SS BOND : bond 0.00507 ( 6) SS BOND : angle 1.08619 ( 12) covalent geometry : bond 0.00319 (10566) covalent geometry : angle 0.63006 (14366) *********************** 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 427 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 425 time to evaluate : 1.084 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 29 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7981 (pt0) REVERT: A 30 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7755 (tptm) REVERT: A 40 PHE cc_start: 0.9042 (t80) cc_final: 0.8495 (t80) REVERT: A 53 ASN cc_start: 0.8679 (m-40) cc_final: 0.8303 (m110) REVERT: A 68 MET cc_start: 0.9293 (ppp) cc_final: 0.8814 (ppp) REVERT: A 71 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8617 (mt-10) REVERT: A 87 HIS cc_start: 0.8227 (m-70) cc_final: 0.7857 (t70) REVERT: A 100 ARG cc_start: 0.8561 (ttt180) cc_final: 0.8340 (tmm-80) REVERT: A 132 ARG cc_start: 0.9320 (tmt-80) cc_final: 0.8889 (tpt90) REVERT: A 136 LEU cc_start: 0.9507 (tt) cc_final: 0.9068 (tt) REVERT: A 139 ASN cc_start: 0.8791 (t0) cc_final: 0.8553 (t0) REVERT: A 149 SER cc_start: 0.9092 (t) cc_final: 0.8647 (p) REVERT: A 152 ASP cc_start: 0.8995 (m-30) cc_final: 0.8730 (m-30) REVERT: A 167 ARG cc_start: 0.9563 (mpp-170) cc_final: 0.9250 (ptt-90) REVERT: A 203 LYS cc_start: 0.9314 (mttt) cc_final: 0.8980 (mttt) REVERT: A 212 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8493 (pm20) REVERT: B 24 VAL cc_start: 0.9173 (p) cc_final: 0.8871 (p) REVERT: B 39 MET cc_start: 0.9571 (tpp) cc_final: 0.8932 (tpt) REVERT: B 51 ASP cc_start: 0.9098 (t0) cc_final: 0.8697 (t0) REVERT: B 55 MET cc_start: 0.9253 (mtm) cc_final: 0.8100 (mtm) REVERT: B 68 MET cc_start: 0.8974 (mtp) cc_final: 0.8708 (mtp) REVERT: B 84 HIS cc_start: 0.9493 (m90) cc_final: 0.8822 (t-90) REVERT: B 96 MET cc_start: 0.9021 (mmp) cc_final: 0.8455 (mpp) REVERT: B 103 ASP cc_start: 0.9197 (m-30) cc_final: 0.8799 (m-30) REVERT: B 112 GLN cc_start: 0.9735 (tp40) cc_final: 0.9384 (tp-100) REVERT: B 135 ILE cc_start: 0.9461 (pt) cc_final: 0.9258 (pt) REVERT: B 215 MET cc_start: 0.8791 (mtm) cc_final: 0.8564 (mtm) REVERT: C 52 LEU cc_start: 0.9624 (mp) cc_final: 0.9409 (mp) REVERT: C 68 MET cc_start: 0.9367 (mtp) cc_final: 0.8975 (mtt) REVERT: C 103 ASP cc_start: 0.9152 (m-30) cc_final: 0.8656 (m-30) REVERT: C 104 ILE cc_start: 0.8600 (tt) cc_final: 0.8173 (pt) REVERT: C 140 LYS cc_start: 0.9457 (mtpp) cc_final: 0.9241 (mtpp) REVERT: C 158 LYS cc_start: 0.9153 (mmmt) cc_final: 0.8848 (mmmm) REVERT: C 167 ARG cc_start: 0.9412 (ptp90) cc_final: 0.8545 (ptp90) REVERT: C 168 PHE cc_start: 0.9479 (t80) cc_final: 0.9180 (t80) REVERT: C 182 LYS cc_start: 0.8422 (ptpt) cc_final: 0.8177 (ptpt) REVERT: D 10 MET cc_start: 0.7018 (mmp) cc_final: 0.5947 (tpp) REVERT: D 23 TRP cc_start: 0.9101 (t-100) cc_final: 0.8735 (t-100) REVERT: D 53 ASN cc_start: 0.8538 (m-40) cc_final: 0.8162 (m110) REVERT: D 114 GLN cc_start: 0.9445 (pt0) cc_final: 0.9167 (pp30) REVERT: D 118 MET cc_start: 0.9006 (ptp) cc_final: 0.8792 (mmm) REVERT: D 128 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7919 (tm-30) REVERT: D 129 ILE cc_start: 0.9024 (mt) cc_final: 0.8649 (tt) REVERT: D 131 LYS cc_start: 0.9491 (tttt) cc_final: 0.9246 (ptpt) REVERT: D 164 TYR cc_start: 0.8593 (t80) cc_final: 0.7947 (t80) REVERT: D 169 TYR cc_start: 0.9109 (m-80) cc_final: 0.8617 (m-80) REVERT: D 212 GLU cc_start: 0.9095 (pt0) cc_final: 0.8528 (pm20) REVERT: D 214 MET cc_start: 0.8792 (mmp) cc_final: 0.8541 (mmm) REVERT: E 28 GLU cc_start: 0.8974 (pt0) cc_final: 0.8596 (pp20) REVERT: E 35 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8023 (tm-30) REVERT: E 43 LEU cc_start: 0.9118 (mt) cc_final: 0.8918 (mt) REVERT: E 68 MET cc_start: 0.8824 (mtp) cc_final: 0.8504 (tpp) REVERT: E 84 HIS cc_start: 0.9425 (m90) cc_final: 0.8789 (t-90) REVERT: E 96 MET cc_start: 0.8576 (mmp) cc_final: 0.7302 (mpp) REVERT: E 140 LYS cc_start: 0.9358 (mttt) cc_final: 0.9034 (mtpt) REVERT: E 141 ILE cc_start: 0.9173 (mt) cc_final: 0.8808 (mt) REVERT: E 144 MET cc_start: 0.8478 (ppp) cc_final: 0.8017 (ppp) REVERT: F 68 MET cc_start: 0.9329 (mtp) cc_final: 0.8983 (mtt) REVERT: F 118 MET cc_start: 0.7658 (mmp) cc_final: 0.7305 (mmm) REVERT: F 131 LYS cc_start: 0.9453 (ttmt) cc_final: 0.9163 (tttt) REVERT: F 140 LYS cc_start: 0.9465 (mtpp) cc_final: 0.9260 (mtpp) REVERT: F 164 TYR cc_start: 0.8709 (t80) cc_final: 0.8203 (t80) REVERT: F 168 PHE cc_start: 0.9501 (t80) cc_final: 0.9067 (t80) REVERT: F 185 MET cc_start: 0.8832 (mmp) cc_final: 0.8579 (mmm) REVERT: F 190 LEU cc_start: 0.9430 (mt) cc_final: 0.8815 (mt) REVERT: F 213 GLU cc_start: 0.9076 (pt0) cc_final: 0.8808 (pt0) REVERT: F 215 MET cc_start: 0.9447 (tmm) cc_final: 0.9234 (tmm) outliers start: 2 outliers final: 0 residues processed: 427 average time/residue: 0.3011 time to fit residues: 172.9304 Evaluate side-chains 332 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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: 20.0000 chunk 82 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 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 12 HIS ** 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.086986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.060486 restraints weight = 71723.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.063883 restraints weight = 40120.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.066406 restraints weight = 27130.295| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.6224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10572 Z= 0.141 Angle : 0.636 6.870 14378 Z= 0.333 Chirality : 0.046 0.188 1604 Planarity : 0.005 0.043 1882 Dihedral : 4.060 19.977 1404 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: 0.39 (0.22), residues: 1310 helix: 0.76 (0.17), residues: 848 sheet: None (None), residues: 0 loop : -0.54 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 23 HIS 0.004 0.001 HIS D 62 PHE 0.025 0.002 PHE E 168 TYR 0.038 0.002 TYR D 145 ARG 0.008 0.001 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 577) hydrogen bonds : angle 3.98976 ( 1731) SS BOND : bond 0.00317 ( 6) SS BOND : angle 1.27626 ( 12) covalent geometry : bond 0.00316 (10566) covalent geometry : angle 0.63549 (14366) *********************** 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 : 1.233 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: A 29 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8029 (mt-10) REVERT: A 30 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7774 (tptm) REVERT: A 40 PHE cc_start: 0.9050 (t80) cc_final: 0.8564 (t80) REVERT: A 53 ASN cc_start: 0.8699 (m-40) cc_final: 0.8326 (m110) REVERT: A 68 MET cc_start: 0.9309 (ppp) cc_final: 0.8856 (ppp) REVERT: A 71 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8601 (mt-10) REVERT: A 87 HIS cc_start: 0.8214 (m-70) cc_final: 0.7858 (t70) REVERT: A 100 ARG cc_start: 0.8693 (ttt180) cc_final: 0.8490 (tmm-80) REVERT: A 132 ARG cc_start: 0.9286 (tmt-80) cc_final: 0.8862 (tpt90) REVERT: A 136 LEU cc_start: 0.9489 (tt) cc_final: 0.9071 (tt) REVERT: A 139 ASN cc_start: 0.8770 (t0) cc_final: 0.8511 (t0) REVERT: A 149 SER cc_start: 0.9141 (t) cc_final: 0.8713 (p) REVERT: A 152 ASP cc_start: 0.9058 (m-30) cc_final: 0.8777 (m-30) REVERT: A 167 ARG cc_start: 0.9507 (mpp-170) cc_final: 0.9130 (ptt-90) REVERT: A 203 LYS cc_start: 0.9309 (mttt) cc_final: 0.8996 (mttt) REVERT: A 212 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8482 (pm20) REVERT: B 28 GLU cc_start: 0.8952 (pt0) cc_final: 0.8714 (pt0) REVERT: B 39 MET cc_start: 0.9578 (tpp) cc_final: 0.8916 (tpt) REVERT: B 51 ASP cc_start: 0.9131 (t0) cc_final: 0.8670 (t0) REVERT: B 55 MET cc_start: 0.9239 (mtm) cc_final: 0.8028 (mtm) REVERT: B 84 HIS cc_start: 0.9495 (m90) cc_final: 0.8836 (t-90) REVERT: B 96 MET cc_start: 0.9045 (mmp) cc_final: 0.8526 (mpp) REVERT: B 103 ASP cc_start: 0.9219 (m-30) cc_final: 0.8852 (m-30) REVERT: B 112 GLN cc_start: 0.9734 (tp40) cc_final: 0.9371 (tp-100) REVERT: B 215 MET cc_start: 0.8792 (mtm) cc_final: 0.8577 (mtm) REVERT: C 52 LEU cc_start: 0.9642 (mp) cc_final: 0.9361 (mp) REVERT: C 68 MET cc_start: 0.9378 (mtp) cc_final: 0.9014 (mtt) REVERT: C 103 ASP cc_start: 0.9066 (m-30) cc_final: 0.7950 (t70) REVERT: C 104 ILE cc_start: 0.8677 (tt) cc_final: 0.8187 (pt) REVERT: C 110 THR cc_start: 0.9499 (m) cc_final: 0.9216 (p) REVERT: C 140 LYS cc_start: 0.9462 (mtpp) cc_final: 0.9178 (mtpp) REVERT: C 158 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8800 (mmmm) REVERT: C 167 ARG cc_start: 0.9406 (ptp90) cc_final: 0.9162 (ptp90) REVERT: C 168 PHE cc_start: 0.9482 (t80) cc_final: 0.9133 (t80) REVERT: C 182 LYS cc_start: 0.8390 (ptpt) cc_final: 0.8148 (ptpt) REVERT: C 190 LEU cc_start: 0.9421 (mt) cc_final: 0.9193 (mt) REVERT: D 40 PHE cc_start: 0.9012 (t80) cc_final: 0.8444 (t80) REVERT: D 53 ASN cc_start: 0.8613 (m-40) cc_final: 0.8239 (m110) REVERT: D 96 MET cc_start: 0.0680 (mmt) cc_final: 0.0313 (mpp) REVERT: D 100 ARG cc_start: 0.8842 (ttt180) cc_final: 0.8221 (ttm-80) REVERT: D 129 ILE cc_start: 0.9060 (mt) cc_final: 0.8790 (tt) REVERT: D 131 LYS cc_start: 0.9524 (tttt) cc_final: 0.9308 (tttt) REVERT: D 136 LEU cc_start: 0.9661 (tt) cc_final: 0.9097 (tt) REVERT: D 164 TYR cc_start: 0.8559 (t80) cc_final: 0.7923 (t80) REVERT: D 169 TYR cc_start: 0.9189 (m-80) cc_final: 0.8894 (m-80) REVERT: D 212 GLU cc_start: 0.9009 (pt0) cc_final: 0.8445 (pm20) REVERT: E 25 LYS cc_start: 0.9342 (mtmm) cc_final: 0.8896 (mttp) REVERT: E 35 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8125 (tm-30) REVERT: E 68 MET cc_start: 0.8847 (mtp) cc_final: 0.8565 (tpp) REVERT: E 84 HIS cc_start: 0.9466 (m90) cc_final: 0.8878 (t-90) REVERT: E 96 MET cc_start: 0.8624 (mmp) cc_final: 0.7530 (mpp) REVERT: E 103 ASP cc_start: 0.9095 (m-30) cc_final: 0.8884 (m-30) REVERT: E 140 LYS cc_start: 0.9442 (mttt) cc_final: 0.9134 (mtpt) REVERT: E 141 ILE cc_start: 0.9161 (mt) cc_final: 0.8799 (mt) REVERT: E 144 MET cc_start: 0.8541 (ppp) cc_final: 0.8073 (ppp) REVERT: E 170 LYS cc_start: 0.9163 (pttt) cc_final: 0.8916 (pttm) REVERT: E 215 MET cc_start: 0.8755 (ptp) cc_final: 0.8205 (ptp) REVERT: F 52 LEU cc_start: 0.9813 (mp) cc_final: 0.9423 (mp) REVERT: F 68 MET cc_start: 0.9330 (mtp) cc_final: 0.8936 (mtt) REVERT: F 118 MET cc_start: 0.7769 (mmp) cc_final: 0.7407 (mmm) REVERT: F 140 LYS cc_start: 0.9453 (mtpp) cc_final: 0.9237 (mtpp) REVERT: F 164 TYR cc_start: 0.8746 (t80) cc_final: 0.8268 (t80) REVERT: F 168 PHE cc_start: 0.9535 (t80) cc_final: 0.9082 (t80) REVERT: F 185 MET cc_start: 0.8955 (mmp) cc_final: 0.8718 (mmm) REVERT: F 190 LEU cc_start: 0.9386 (mt) cc_final: 0.8773 (mt) REVERT: F 199 LYS cc_start: 0.9012 (ptmt) cc_final: 0.8793 (pttm) REVERT: F 213 GLU cc_start: 0.9127 (pt0) cc_final: 0.8922 (pt0) outliers start: 2 outliers final: 0 residues processed: 410 average time/residue: 0.2533 time to fit residues: 138.7358 Evaluate side-chains 331 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 22 optimal weight: 0.0040 overall best weight: 5.6000 ------------------------------------------------------------------------------- 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** D 95 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 ASN ** 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 = 0.3367 r_free = 0.3367 target = 0.083215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.056514 restraints weight = 82467.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.060006 restraints weight = 43936.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.062598 restraints weight = 29190.781| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.6707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10572 Z= 0.190 Angle : 0.682 8.667 14378 Z= 0.361 Chirality : 0.047 0.242 1604 Planarity : 0.005 0.055 1882 Dihedral : 4.209 19.847 1404 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.18 % Allowed : 1.50 % Favored : 98.32 % 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: 0.12 (0.22), residues: 1310 helix: 0.44 (0.17), residues: 868 sheet: None (None), residues: 0 loop : -0.44 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 23 HIS 0.006 0.002 HIS D 62 PHE 0.016 0.002 PHE B 168 TYR 0.027 0.002 TYR D 130 ARG 0.015 0.001 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 577) hydrogen bonds : angle 4.27567 ( 1731) SS BOND : bond 0.00456 ( 6) SS BOND : angle 1.54745 ( 12) covalent geometry : bond 0.00404 (10566) covalent geometry : angle 0.68082 (14366) *********************** 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 : 1.149 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: A 10 MET cc_start: 0.7231 (mmp) cc_final: 0.6733 (tpp) REVERT: A 29 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8109 (mt-10) REVERT: A 30 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7718 (tptm) REVERT: A 40 PHE cc_start: 0.9108 (t80) cc_final: 0.8692 (t80) REVERT: A 53 ASN cc_start: 0.8770 (m-40) cc_final: 0.8424 (m110) REVERT: A 68 MET cc_start: 0.9347 (ppp) cc_final: 0.8938 (ppp) REVERT: A 71 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8662 (mt-10) REVERT: A 100 ARG cc_start: 0.8805 (ttt180) cc_final: 0.8272 (tmm-80) REVERT: A 103 ASP cc_start: 0.9214 (m-30) cc_final: 0.8339 (m-30) REVERT: A 131 LYS cc_start: 0.9400 (ptpp) cc_final: 0.9172 (pttt) REVERT: A 132 ARG cc_start: 0.9341 (tmt-80) cc_final: 0.8893 (tpt90) REVERT: A 136 LEU cc_start: 0.9517 (tt) cc_final: 0.9122 (tt) REVERT: A 139 ASN cc_start: 0.8851 (t0) cc_final: 0.8610 (t0) REVERT: A 149 SER cc_start: 0.9286 (t) cc_final: 0.8853 (p) REVERT: A 152 ASP cc_start: 0.9180 (m-30) cc_final: 0.8873 (m-30) REVERT: A 167 ARG cc_start: 0.9536 (mpp-170) cc_final: 0.9056 (ptt-90) REVERT: A 192 GLN cc_start: 0.9366 (mp10) cc_final: 0.9063 (mp10) REVERT: A 203 LYS cc_start: 0.9340 (mttt) cc_final: 0.9014 (mttt) REVERT: A 212 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8563 (pm20) REVERT: A 214 MET cc_start: 0.8809 (mmp) cc_final: 0.8569 (mmt) REVERT: B 2 ILE cc_start: 0.9010 (tp) cc_final: 0.8715 (tp) REVERT: B 28 GLU cc_start: 0.8995 (pt0) cc_final: 0.8740 (pt0) REVERT: B 51 ASP cc_start: 0.9251 (t0) cc_final: 0.8772 (t0) REVERT: B 55 MET cc_start: 0.9227 (mtm) cc_final: 0.8087 (mtm) REVERT: B 68 MET cc_start: 0.9151 (ttm) cc_final: 0.8572 (tpp) REVERT: B 96 MET cc_start: 0.9123 (mmp) cc_final: 0.8637 (mpp) REVERT: B 103 ASP cc_start: 0.9208 (m-30) cc_final: 0.8935 (m-30) REVERT: B 112 GLN cc_start: 0.9760 (tp40) cc_final: 0.9422 (tp-100) REVERT: B 215 MET cc_start: 0.8887 (mtm) cc_final: 0.8593 (mtm) REVERT: C 52 LEU cc_start: 0.9672 (mp) cc_final: 0.9397 (mp) REVERT: C 68 MET cc_start: 0.9363 (mtp) cc_final: 0.8995 (mtt) REVERT: C 103 ASP cc_start: 0.9085 (m-30) cc_final: 0.8018 (t70) REVERT: C 104 ILE cc_start: 0.8725 (tt) cc_final: 0.8201 (pt) REVERT: C 140 LYS cc_start: 0.9476 (mtpp) cc_final: 0.9224 (mtpp) REVERT: C 152 ASP cc_start: 0.9244 (m-30) cc_final: 0.9001 (m-30) REVERT: C 158 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8895 (mmmm) REVERT: C 167 ARG cc_start: 0.9415 (ptp90) cc_final: 0.9160 (ptp90) REVERT: C 168 PHE cc_start: 0.9529 (t80) cc_final: 0.9158 (t80) REVERT: C 190 LEU cc_start: 0.9435 (mt) cc_final: 0.9227 (mt) REVERT: D 29 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8034 (mt-10) REVERT: D 39 MET cc_start: 0.9087 (mtp) cc_final: 0.8623 (mmm) REVERT: D 53 ASN cc_start: 0.8678 (m-40) cc_final: 0.8271 (m110) REVERT: D 96 MET cc_start: 0.1221 (mmt) cc_final: 0.0827 (mpp) REVERT: D 103 ASP cc_start: 0.9342 (m-30) cc_final: 0.9077 (m-30) REVERT: D 126 VAL cc_start: 0.6884 (t) cc_final: 0.6348 (t) REVERT: D 129 ILE cc_start: 0.9160 (mt) cc_final: 0.8843 (tt) REVERT: D 132 ARG cc_start: 0.9306 (tmt-80) cc_final: 0.8837 (tpt90) REVERT: D 136 LEU cc_start: 0.9606 (tt) cc_final: 0.9249 (tt) REVERT: D 164 TYR cc_start: 0.8585 (t80) cc_final: 0.8052 (t80) REVERT: D 168 PHE cc_start: 0.9164 (t80) cc_final: 0.8809 (t80) REVERT: D 203 LYS cc_start: 0.9375 (mttt) cc_final: 0.9107 (mttt) REVERT: D 212 GLU cc_start: 0.9058 (pt0) cc_final: 0.8554 (pm20) REVERT: E 30 LYS cc_start: 0.9099 (tptp) cc_final: 0.8898 (tptp) REVERT: E 35 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8254 (tm-30) REVERT: E 68 MET cc_start: 0.8801 (mtp) cc_final: 0.8501 (tpp) REVERT: E 84 HIS cc_start: 0.9463 (m90) cc_final: 0.8854 (t-90) REVERT: E 96 MET cc_start: 0.8761 (mmp) cc_final: 0.7763 (mpp) REVERT: E 103 ASP cc_start: 0.9126 (m-30) cc_final: 0.8898 (m-30) REVERT: E 140 LYS cc_start: 0.9425 (mttt) cc_final: 0.9056 (tttt) REVERT: E 141 ILE cc_start: 0.9292 (mt) cc_final: 0.9031 (mt) REVERT: E 144 MET cc_start: 0.8652 (ppp) cc_final: 0.8130 (ppp) REVERT: E 170 LYS cc_start: 0.9179 (pttt) cc_final: 0.8678 (pttt) REVERT: F 52 LEU cc_start: 0.9746 (mp) cc_final: 0.9505 (mp) REVERT: F 68 MET cc_start: 0.9311 (mtp) cc_final: 0.9047 (mtt) REVERT: F 104 ILE cc_start: 0.8861 (tt) cc_final: 0.8488 (pt) REVERT: F 118 MET cc_start: 0.7976 (mmp) cc_final: 0.7679 (mmm) REVERT: F 139 ASN cc_start: 0.9491 (t0) cc_final: 0.9275 (m110) REVERT: F 140 LYS cc_start: 0.9487 (mtpp) cc_final: 0.9264 (mtpp) REVERT: F 154 ARG cc_start: 0.8970 (ttm110) cc_final: 0.8673 (ttm110) REVERT: F 164 TYR cc_start: 0.8824 (t80) cc_final: 0.8311 (t80) REVERT: F 168 PHE cc_start: 0.9570 (t80) cc_final: 0.9030 (t80) REVERT: F 190 LEU cc_start: 0.9336 (mt) cc_final: 0.8777 (mt) REVERT: F 213 GLU cc_start: 0.9154 (pt0) cc_final: 0.8938 (pt0) REVERT: F 215 MET cc_start: 0.9481 (tmm) cc_final: 0.9223 (tmm) outliers start: 2 outliers final: 0 residues processed: 409 average time/residue: 0.2416 time to fit residues: 132.7198 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 : 1.248 ------------------------------------------------------------------------------- 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: 3.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 61 optimal weight: 0.0470 overall best weight: 2.0086 ------------------------------------------------------------------------------- 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 A 95 GLN B 84 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN D 95 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.058615 restraints weight = 77280.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.062186 restraints weight = 41691.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.064828 restraints weight = 27857.115| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.6838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10572 Z= 0.134 Angle : 0.680 7.878 14378 Z= 0.355 Chirality : 0.047 0.340 1604 Planarity : 0.005 0.044 1882 Dihedral : 4.244 20.483 1404 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.18 % Allowed : 0.97 % Favored : 98.85 % 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: 0.36 (0.22), residues: 1310 helix: 0.64 (0.17), residues: 858 sheet: None (None), residues: 0 loop : -0.36 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 117 HIS 0.004 0.001 HIS A 62 PHE 0.014 0.002 PHE E 168 TYR 0.024 0.002 TYR D 130 ARG 0.010 0.001 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 577) hydrogen bonds : angle 4.20431 ( 1731) SS BOND : bond 0.00839 ( 6) SS BOND : angle 1.44179 ( 12) covalent geometry : bond 0.00306 (10566) covalent geometry : angle 0.67913 (14366) *********************** 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 393 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 391 time to evaluate : 1.211 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: A 10 MET cc_start: 0.7295 (mmp) cc_final: 0.6787 (tpp) REVERT: A 29 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7911 (mt-10) REVERT: A 30 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7684 (tptm) REVERT: A 40 PHE cc_start: 0.9038 (t80) cc_final: 0.8599 (t80) REVERT: A 53 ASN cc_start: 0.8715 (m-40) cc_final: 0.8377 (m110) REVERT: A 68 MET cc_start: 0.9339 (ppp) cc_final: 0.8969 (ppp) REVERT: A 71 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8626 (mt-10) REVERT: A 100 ARG cc_start: 0.8827 (ttt180) cc_final: 0.8264 (tmm-80) REVERT: A 103 ASP cc_start: 0.9245 (m-30) cc_final: 0.8367 (m-30) REVERT: A 132 ARG cc_start: 0.9330 (tmt-80) cc_final: 0.8917 (tpt90) REVERT: A 136 LEU cc_start: 0.9485 (tt) cc_final: 0.9065 (tt) REVERT: A 139 ASN cc_start: 0.8831 (t0) cc_final: 0.8590 (t0) REVERT: A 149 SER cc_start: 0.9299 (t) cc_final: 0.8912 (p) REVERT: A 152 ASP cc_start: 0.9223 (m-30) cc_final: 0.8991 (m-30) REVERT: A 192 GLN cc_start: 0.9352 (mp10) cc_final: 0.9085 (mp10) REVERT: A 203 LYS cc_start: 0.9329 (mttt) cc_final: 0.9016 (mttt) REVERT: A 212 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8538 (pm20) REVERT: B 28 GLU cc_start: 0.9083 (pt0) cc_final: 0.8785 (pt0) REVERT: B 39 MET cc_start: 0.9567 (tpp) cc_final: 0.9159 (tmm) REVERT: B 51 ASP cc_start: 0.9153 (t0) cc_final: 0.8580 (t0) REVERT: B 55 MET cc_start: 0.9230 (mtm) cc_final: 0.8160 (mtm) REVERT: B 68 MET cc_start: 0.9102 (ttm) cc_final: 0.8570 (tpp) REVERT: B 84 HIS cc_start: 0.9460 (m90) cc_final: 0.8748 (t-90) REVERT: B 96 MET cc_start: 0.9169 (mmp) cc_final: 0.8760 (mpp) REVERT: B 103 ASP cc_start: 0.9261 (m-30) cc_final: 0.8915 (m-30) REVERT: B 112 GLN cc_start: 0.9756 (tp40) cc_final: 0.9419 (tp-100) REVERT: B 215 MET cc_start: 0.8843 (mtm) cc_final: 0.8525 (mtm) REVERT: C 52 LEU cc_start: 0.9665 (mp) cc_final: 0.9382 (mp) REVERT: C 68 MET cc_start: 0.9375 (mtp) cc_final: 0.8983 (mtt) REVERT: C 103 ASP cc_start: 0.9021 (m-30) cc_final: 0.8173 (t70) REVERT: C 104 ILE cc_start: 0.8714 (tt) cc_final: 0.8176 (pt) REVERT: C 140 LYS cc_start: 0.9460 (mtpp) cc_final: 0.9186 (mtpp) REVERT: C 158 LYS cc_start: 0.9227 (mmmt) cc_final: 0.8888 (mmmm) REVERT: C 167 ARG cc_start: 0.9379 (ptp90) cc_final: 0.9148 (ptp90) REVERT: C 168 PHE cc_start: 0.9509 (t80) cc_final: 0.9127 (t80) REVERT: C 182 LYS cc_start: 0.8372 (ptpt) cc_final: 0.8152 (ptpt) REVERT: C 190 LEU cc_start: 0.9395 (mt) cc_final: 0.9144 (mt) REVERT: D 29 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7869 (mt-10) REVERT: D 32 PHE cc_start: 0.7638 (m-80) cc_final: 0.7386 (m-80) REVERT: D 53 ASN cc_start: 0.8563 (m-40) cc_final: 0.8139 (m110) REVERT: D 96 MET cc_start: 0.1007 (mmt) cc_final: 0.0645 (mpp) REVERT: D 100 ARG cc_start: 0.8897 (ttt180) cc_final: 0.8602 (tmm-80) REVERT: D 114 GLN cc_start: 0.9409 (pt0) cc_final: 0.9186 (pp30) REVERT: D 129 ILE cc_start: 0.9142 (mt) cc_final: 0.8810 (tt) REVERT: D 132 ARG cc_start: 0.9321 (tmt-80) cc_final: 0.8926 (tpt90) REVERT: D 136 LEU cc_start: 0.9641 (tt) cc_final: 0.9238 (tt) REVERT: D 141 ILE cc_start: 0.9587 (mm) cc_final: 0.9229 (mm) REVERT: D 164 TYR cc_start: 0.8602 (t80) cc_final: 0.8011 (t80) REVERT: D 168 PHE cc_start: 0.9127 (t80) cc_final: 0.8850 (t80) REVERT: D 169 TYR cc_start: 0.9335 (m-80) cc_final: 0.8949 (m-80) REVERT: D 212 GLU cc_start: 0.8991 (pt0) cc_final: 0.8512 (pm20) REVERT: E 35 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8220 (tm-30) REVERT: E 68 MET cc_start: 0.8773 (mtp) cc_final: 0.8546 (tpp) REVERT: E 79 GLU cc_start: 0.9126 (pp20) cc_final: 0.8894 (pp20) REVERT: E 84 HIS cc_start: 0.9478 (m90) cc_final: 0.8835 (t-90) REVERT: E 96 MET cc_start: 0.8688 (mmp) cc_final: 0.7574 (mpp) REVERT: E 103 ASP cc_start: 0.9065 (m-30) cc_final: 0.8856 (m-30) REVERT: E 140 LYS cc_start: 0.9433 (mttt) cc_final: 0.9164 (mtpt) REVERT: E 141 ILE cc_start: 0.9274 (mt) cc_final: 0.8984 (mt) REVERT: E 144 MET cc_start: 0.8597 (ppp) cc_final: 0.8068 (ppp) REVERT: E 211 LEU cc_start: 0.9185 (pt) cc_final: 0.8930 (pt) REVERT: F 52 LEU cc_start: 0.9677 (mp) cc_final: 0.9424 (mp) REVERT: F 68 MET cc_start: 0.9257 (mtp) cc_final: 0.8931 (mtt) REVERT: F 71 GLU cc_start: 0.8726 (pp20) cc_final: 0.8342 (pp20) REVERT: F 104 ILE cc_start: 0.8977 (tt) cc_final: 0.8543 (pt) REVERT: F 118 MET cc_start: 0.8074 (mmp) cc_final: 0.7753 (mmm) REVERT: F 140 LYS cc_start: 0.9447 (mtpp) cc_final: 0.9232 (mtpp) REVERT: F 159 GLU cc_start: 0.8748 (pt0) cc_final: 0.7813 (mp0) REVERT: F 164 TYR cc_start: 0.8673 (t80) cc_final: 0.8282 (t80) REVERT: F 168 PHE cc_start: 0.9563 (t80) cc_final: 0.9000 (t80) REVERT: F 185 MET cc_start: 0.8812 (mmp) cc_final: 0.8566 (mmm) REVERT: F 190 LEU cc_start: 0.9270 (mt) cc_final: 0.8910 (mt) REVERT: F 213 GLU cc_start: 0.9178 (pt0) cc_final: 0.8947 (pt0) outliers start: 2 outliers final: 0 residues processed: 393 average time/residue: 0.2400 time to fit residues: 127.5758 Evaluate side-chains 315 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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: 3.9990 chunk 9 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 18 optimal weight: 0.0570 chunk 74 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 95 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN D 95 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 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 = 0.3402 r_free = 0.3402 target = 0.085000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.058961 restraints weight = 70043.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.062357 restraints weight = 39452.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064847 restraints weight = 26674.548| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.7055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10572 Z= 0.145 Angle : 0.676 9.410 14378 Z= 0.352 Chirality : 0.047 0.223 1604 Planarity : 0.005 0.052 1882 Dihedral : 4.277 16.309 1404 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.18 % Allowed : 0.71 % Favored : 99.12 % 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: 0.26 (0.22), residues: 1310 helix: 0.58 (0.17), residues: 858 sheet: None (None), residues: 0 loop : -0.43 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 117 HIS 0.004 0.001 HIS D 62 PHE 0.018 0.002 PHE A 168 TYR 0.028 0.003 TYR D 130 ARG 0.007 0.001 ARG F 100 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 577) hydrogen bonds : angle 4.28686 ( 1731) SS BOND : bond 0.00429 ( 6) SS BOND : angle 1.23156 ( 12) covalent geometry : bond 0.00329 (10566) covalent geometry : angle 0.67567 (14366) *********************** 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 389 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 387 time to evaluate : 1.232 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: 0.7331 (mmp) cc_final: 0.6773 (tpp) REVERT: A 29 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 30 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7719 (tptm) REVERT: A 40 PHE cc_start: 0.9036 (t80) cc_final: 0.8618 (t80) REVERT: A 53 ASN cc_start: 0.8733 (m-40) cc_final: 0.8390 (m110) REVERT: A 68 MET cc_start: 0.9352 (ppp) cc_final: 0.9009 (ppp) REVERT: A 71 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8697 (mt-10) REVERT: A 100 ARG cc_start: 0.8818 (ttt180) cc_final: 0.8242 (tmm-80) REVERT: A 103 ASP cc_start: 0.9168 (m-30) cc_final: 0.8306 (m-30) REVERT: A 132 ARG cc_start: 0.9274 (tmt-80) cc_final: 0.8887 (tpt90) REVERT: A 136 LEU cc_start: 0.9448 (tt) cc_final: 0.9088 (tt) REVERT: A 149 SER cc_start: 0.9364 (t) cc_final: 0.8943 (p) REVERT: A 152 ASP cc_start: 0.9204 (m-30) cc_final: 0.8866 (m-30) REVERT: A 167 ARG cc_start: 0.9334 (mtm110) cc_final: 0.8986 (mtm-85) REVERT: A 203 LYS cc_start: 0.9339 (mttt) cc_final: 0.8995 (mtmt) REVERT: A 212 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8451 (pm20) REVERT: B 28 GLU cc_start: 0.9115 (pt0) cc_final: 0.8751 (pt0) REVERT: B 39 MET cc_start: 0.9589 (tpp) cc_final: 0.9126 (tmm) REVERT: B 51 ASP cc_start: 0.9168 (t0) cc_final: 0.8700 (t0) REVERT: B 55 MET cc_start: 0.9085 (mtm) cc_final: 0.8375 (mtm) REVERT: B 68 MET cc_start: 0.9102 (ttm) cc_final: 0.8560 (tpp) REVERT: B 84 HIS cc_start: 0.9411 (m90) cc_final: 0.9122 (m-70) REVERT: B 96 MET cc_start: 0.9152 (mmp) cc_final: 0.8809 (mpp) REVERT: B 103 ASP cc_start: 0.9222 (m-30) cc_final: 0.8920 (m-30) REVERT: B 112 GLN cc_start: 0.9754 (tp40) cc_final: 0.9425 (tp-100) REVERT: B 144 MET cc_start: 0.8576 (tmm) cc_final: 0.8353 (tmm) REVERT: B 170 LYS cc_start: 0.9465 (tmmt) cc_final: 0.9088 (pttt) REVERT: B 215 MET cc_start: 0.8777 (mtm) cc_final: 0.8486 (mtm) REVERT: C 52 LEU cc_start: 0.9640 (mp) cc_final: 0.9413 (mp) REVERT: C 68 MET cc_start: 0.9372 (mtp) cc_final: 0.9026 (mtt) REVERT: C 103 ASP cc_start: 0.9028 (m-30) cc_final: 0.8532 (m-30) REVERT: C 104 ILE cc_start: 0.8790 (tt) cc_final: 0.8299 (pt) REVERT: C 128 GLU cc_start: 0.9481 (mp0) cc_final: 0.9197 (mp0) REVERT: C 130 TYR cc_start: 0.9389 (t80) cc_final: 0.9184 (t80) REVERT: C 140 LYS cc_start: 0.9492 (mtpp) cc_final: 0.9226 (mtpp) REVERT: C 151 LEU cc_start: 0.9398 (mm) cc_final: 0.9192 (mm) REVERT: C 158 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8887 (mmmm) REVERT: C 167 ARG cc_start: 0.9394 (ptp90) cc_final: 0.9193 (ptp90) REVERT: C 168 PHE cc_start: 0.9461 (t80) cc_final: 0.9081 (t80) REVERT: C 182 LYS cc_start: 0.8546 (ptpt) cc_final: 0.8282 (ptpt) REVERT: C 190 LEU cc_start: 0.9354 (mt) cc_final: 0.9114 (mt) REVERT: D 10 MET cc_start: 0.7230 (mmp) cc_final: 0.6246 (tpp) REVERT: D 29 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7827 (mt-10) REVERT: D 32 PHE cc_start: 0.7808 (m-80) cc_final: 0.7556 (m-80) REVERT: D 39 MET cc_start: 0.8952 (mmm) cc_final: 0.8704 (mmm) REVERT: D 53 ASN cc_start: 0.8630 (m-40) cc_final: 0.8205 (m110) REVERT: D 96 MET cc_start: 0.1079 (mmt) cc_final: 0.0767 (mpp) REVERT: D 100 ARG cc_start: 0.8906 (ttt180) cc_final: 0.8355 (ttm170) REVERT: D 128 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8181 (tm-30) REVERT: D 129 ILE cc_start: 0.9186 (mt) cc_final: 0.8855 (tt) REVERT: D 132 ARG cc_start: 0.9281 (tmt-80) cc_final: 0.8852 (tpt90) REVERT: D 136 LEU cc_start: 0.9597 (tt) cc_final: 0.9249 (tt) REVERT: D 164 TYR cc_start: 0.8566 (t80) cc_final: 0.7980 (t80) REVERT: D 168 PHE cc_start: 0.9123 (t80) cc_final: 0.8837 (t80) REVERT: D 169 TYR cc_start: 0.9279 (m-80) cc_final: 0.8872 (m-80) REVERT: D 203 LYS cc_start: 0.9482 (mttt) cc_final: 0.9130 (mttt) REVERT: D 215 MET cc_start: 0.8770 (ptm) cc_final: 0.8463 (ppp) REVERT: E 35 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8277 (tm-30) REVERT: E 68 MET cc_start: 0.8768 (mtp) cc_final: 0.8302 (tpp) REVERT: E 84 HIS cc_start: 0.9439 (m90) cc_final: 0.8816 (t-90) REVERT: E 96 MET cc_start: 0.8645 (mmp) cc_final: 0.7626 (mpp) REVERT: E 103 ASP cc_start: 0.9057 (m-30) cc_final: 0.8827 (m-30) REVERT: E 124 ILE cc_start: 0.8493 (mm) cc_final: 0.7998 (mm) REVERT: E 140 LYS cc_start: 0.9457 (mttt) cc_final: 0.9121 (mtpt) REVERT: E 141 ILE cc_start: 0.9283 (mt) cc_final: 0.8997 (mt) REVERT: E 144 MET cc_start: 0.8642 (ppp) cc_final: 0.8154 (ppp) REVERT: E 170 LYS cc_start: 0.9165 (pttt) cc_final: 0.8678 (pttt) REVERT: F 52 LEU cc_start: 0.9691 (mp) cc_final: 0.9415 (mp) REVERT: F 68 MET cc_start: 0.9256 (mtp) cc_final: 0.9051 (mtp) REVERT: F 103 ASP cc_start: 0.8909 (m-30) cc_final: 0.8076 (t70) REVERT: F 104 ILE cc_start: 0.9014 (tt) cc_final: 0.8584 (pt) REVERT: F 118 MET cc_start: 0.8128 (mmp) cc_final: 0.7803 (mmm) REVERT: F 140 LYS cc_start: 0.9378 (mtpp) cc_final: 0.9160 (mtpp) REVERT: F 164 TYR cc_start: 0.8741 (t80) cc_final: 0.7810 (t80) REVERT: F 167 ARG cc_start: 0.9449 (ptp90) cc_final: 0.8524 (ptp90) REVERT: F 168 PHE cc_start: 0.9557 (t80) cc_final: 0.8990 (t80) REVERT: F 185 MET cc_start: 0.8868 (mmp) cc_final: 0.8650 (mmm) REVERT: F 190 LEU cc_start: 0.9212 (mt) cc_final: 0.8864 (mt) REVERT: F 213 GLU cc_start: 0.9195 (pt0) cc_final: 0.8982 (pt0) outliers start: 2 outliers final: 0 residues processed: 389 average time/residue: 0.2442 time to fit residues: 128.2465 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 : 1.154 ------------------------------------------------------------------------------- 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: 0.7980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 47 optimal weight: 0.0770 chunk 73 optimal weight: 10.0000 chunk 113 optimal weight: 0.0570 chunk 108 optimal weight: 0.0070 chunk 129 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 95 GLN D 95 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.059624 restraints weight = 95307.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.063504 restraints weight = 46772.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.066390 restraints weight = 30324.565| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.7080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10572 Z= 0.131 Angle : 0.686 7.407 14378 Z= 0.351 Chirality : 0.047 0.164 1604 Planarity : 0.005 0.049 1882 Dihedral : 4.243 20.468 1404 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.18 % Allowed : 0.71 % Favored : 99.12 % 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: 0.41 (0.22), residues: 1310 helix: 0.69 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -0.36 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP F 117 HIS 0.002 0.001 HIS D 62 PHE 0.021 0.002 PHE E 168 TYR 0.028 0.002 TYR D 130 ARG 0.005 0.001 ARG D 167 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 577) hydrogen bonds : angle 4.20042 ( 1731) SS BOND : bond 0.00388 ( 6) SS BOND : angle 1.17525 ( 12) covalent geometry : bond 0.00293 (10566) covalent geometry : angle 0.68497 (14366) *********************** 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 397 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 395 time to evaluate : 1.169 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: 0.7179 (mmp) cc_final: 0.6725 (tpp) REVERT: A 29 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 30 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7838 (tptm) REVERT: A 40 PHE cc_start: 0.8983 (t80) cc_final: 0.8532 (t80) REVERT: A 53 ASN cc_start: 0.8725 (m-40) cc_final: 0.8374 (m110) REVERT: A 68 MET cc_start: 0.9321 (ppp) cc_final: 0.9019 (ppp) REVERT: A 71 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8698 (mt-10) REVERT: A 100 ARG cc_start: 0.8818 (ttt180) cc_final: 0.8253 (tmm-80) REVERT: A 103 ASP cc_start: 0.9146 (m-30) cc_final: 0.8316 (m-30) REVERT: A 131 LYS cc_start: 0.9545 (ptmt) cc_final: 0.9071 (pttt) REVERT: A 149 SER cc_start: 0.9311 (t) cc_final: 0.8947 (p) REVERT: A 152 ASP cc_start: 0.9181 (m-30) cc_final: 0.8940 (m-30) REVERT: A 203 LYS cc_start: 0.9250 (mttt) cc_final: 0.9009 (mttt) REVERT: A 212 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8627 (pm20) REVERT: A 215 MET cc_start: 0.8902 (ptm) cc_final: 0.8606 (ppp) REVERT: B 28 GLU cc_start: 0.9176 (pt0) cc_final: 0.8893 (pt0) REVERT: B 39 MET cc_start: 0.9567 (tpp) cc_final: 0.9122 (tmm) REVERT: B 51 ASP cc_start: 0.9095 (t0) cc_final: 0.8641 (t0) REVERT: B 55 MET cc_start: 0.9020 (mtm) cc_final: 0.8313 (mtm) REVERT: B 68 MET cc_start: 0.9078 (ttm) cc_final: 0.8664 (tpp) REVERT: B 84 HIS cc_start: 0.9410 (m90) cc_final: 0.9139 (m-70) REVERT: B 96 MET cc_start: 0.9167 (mmp) cc_final: 0.8824 (mpp) REVERT: B 103 ASP cc_start: 0.9173 (m-30) cc_final: 0.8874 (m-30) REVERT: B 118 MET cc_start: 0.8560 (mmm) cc_final: 0.8272 (ptm) REVERT: B 170 LYS cc_start: 0.9446 (tmmt) cc_final: 0.9091 (pttt) REVERT: B 215 MET cc_start: 0.8809 (mtm) cc_final: 0.8547 (mtm) REVERT: C 5 ASN cc_start: 0.8028 (t0) cc_final: 0.7271 (p0) REVERT: C 52 LEU cc_start: 0.9582 (mp) cc_final: 0.9364 (mp) REVERT: C 68 MET cc_start: 0.9370 (mtp) cc_final: 0.9038 (mtt) REVERT: C 103 ASP cc_start: 0.8931 (m-30) cc_final: 0.8202 (t70) REVERT: C 104 ILE cc_start: 0.8747 (tt) cc_final: 0.8224 (pt) REVERT: C 140 LYS cc_start: 0.9463 (mtpp) cc_final: 0.9206 (mtpp) REVERT: C 158 LYS cc_start: 0.9235 (mmmt) cc_final: 0.8893 (mmmm) REVERT: C 167 ARG cc_start: 0.9354 (ptp90) cc_final: 0.9146 (ptp90) REVERT: C 168 PHE cc_start: 0.9413 (t80) cc_final: 0.9066 (t80) REVERT: C 182 LYS cc_start: 0.8529 (ptpt) cc_final: 0.8289 (ptpt) REVERT: D 10 MET cc_start: 0.7108 (mmp) cc_final: 0.6300 (tpp) REVERT: D 29 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7696 (mt-10) REVERT: D 53 ASN cc_start: 0.8563 (m-40) cc_final: 0.8039 (m110) REVERT: D 96 MET cc_start: 0.0957 (mmt) cc_final: 0.0628 (mpp) REVERT: D 100 ARG cc_start: 0.8948 (ttt180) cc_final: 0.8289 (ttm170) REVERT: D 128 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8230 (tm-30) REVERT: D 129 ILE cc_start: 0.9202 (mt) cc_final: 0.8906 (tt) REVERT: D 132 ARG cc_start: 0.9316 (tmt-80) cc_final: 0.8844 (tpt90) REVERT: D 136 LEU cc_start: 0.9612 (tt) cc_final: 0.9301 (tt) REVERT: D 164 TYR cc_start: 0.8703 (t80) cc_final: 0.8034 (t80) REVERT: E 35 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8070 (tm-30) REVERT: E 68 MET cc_start: 0.8815 (mtp) cc_final: 0.8415 (tpp) REVERT: E 84 HIS cc_start: 0.9449 (m90) cc_final: 0.8824 (t-90) REVERT: E 96 MET cc_start: 0.8695 (mmp) cc_final: 0.7660 (mpp) REVERT: E 132 ARG cc_start: 0.8855 (ptp-170) cc_final: 0.8573 (ptp90) REVERT: E 140 LYS cc_start: 0.9446 (mttt) cc_final: 0.9131 (mtpt) REVERT: E 141 ILE cc_start: 0.9238 (mt) cc_final: 0.8962 (mt) REVERT: E 144 MET cc_start: 0.8521 (ppp) cc_final: 0.8026 (ppp) REVERT: E 153 ILE cc_start: 0.7223 (mp) cc_final: 0.6914 (tt) REVERT: F 52 LEU cc_start: 0.9683 (mp) cc_final: 0.9421 (mp) REVERT: F 103 ASP cc_start: 0.8618 (m-30) cc_final: 0.8085 (p0) REVERT: F 104 ILE cc_start: 0.9023 (tt) cc_final: 0.8617 (pt) REVERT: F 118 MET cc_start: 0.8226 (mmp) cc_final: 0.7878 (mmm) REVERT: F 159 GLU cc_start: 0.8739 (pt0) cc_final: 0.8252 (pm20) REVERT: F 164 TYR cc_start: 0.8557 (t80) cc_final: 0.8240 (t80) REVERT: F 168 PHE cc_start: 0.9546 (t80) cc_final: 0.8968 (t80) REVERT: F 185 MET cc_start: 0.8742 (mmp) cc_final: 0.8498 (mmp) REVERT: F 190 LEU cc_start: 0.9199 (mt) cc_final: 0.8871 (mt) REVERT: F 213 GLU cc_start: 0.9197 (pt0) cc_final: 0.8994 (pt0) outliers start: 2 outliers final: 0 residues processed: 397 average time/residue: 0.2446 time to fit residues: 130.0374 Evaluate side-chains 313 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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: 10.0000 chunk 38 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 34 optimal weight: 0.0570 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 95 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN C 139 ASN D 95 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.061780 restraints weight = 64187.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.065191 restraints weight = 36925.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.067686 restraints weight = 25337.901| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.7261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10572 Z= 0.135 Angle : 0.714 8.329 14378 Z= 0.371 Chirality : 0.047 0.204 1604 Planarity : 0.005 0.062 1882 Dihedral : 4.197 19.384 1404 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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: 0.36 (0.22), residues: 1310 helix: 0.66 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -0.40 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 23 HIS 0.003 0.001 HIS A 62 PHE 0.054 0.002 PHE A 161 TYR 0.028 0.002 TYR D 130 ARG 0.010 0.001 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 577) hydrogen bonds : angle 4.31004 ( 1731) SS BOND : bond 0.00305 ( 6) SS BOND : angle 1.48742 ( 12) covalent geometry : bond 0.00310 (10566) covalent geometry : angle 0.71330 (14366) ********************** 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 393 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 391 time to evaluate : 1.318 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: A 10 MET cc_start: 0.7253 (mmp) cc_final: 0.6745 (tpp) REVERT: A 29 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7754 (mt-10) REVERT: A 30 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7733 (tptm) REVERT: A 53 ASN cc_start: 0.8722 (m-40) cc_final: 0.8353 (m110) REVERT: A 68 MET cc_start: 0.9330 (ppp) cc_final: 0.8986 (ppp) REVERT: A 71 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8623 (mt-10) REVERT: A 100 ARG cc_start: 0.8873 (ttt180) cc_final: 0.8317 (tmm-80) REVERT: A 103 ASP cc_start: 0.9113 (m-30) cc_final: 0.8342 (m-30) REVERT: A 128 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7834 (tm-30) REVERT: A 131 LYS cc_start: 0.9543 (ptmt) cc_final: 0.9093 (pttt) REVERT: A 132 ARG cc_start: 0.9366 (tmt-80) cc_final: 0.8946 (tpt90) REVERT: A 136 LEU cc_start: 0.9491 (tt) cc_final: 0.9071 (tt) REVERT: A 149 SER cc_start: 0.9324 (t) cc_final: 0.8902 (p) REVERT: A 152 ASP cc_start: 0.9064 (m-30) cc_final: 0.8832 (m-30) REVERT: A 164 TYR cc_start: 0.8655 (t80) cc_final: 0.8126 (t80) REVERT: A 215 MET cc_start: 0.8926 (ptm) cc_final: 0.8566 (ppp) REVERT: B 28 GLU cc_start: 0.9075 (pt0) cc_final: 0.8812 (pt0) REVERT: B 39 MET cc_start: 0.9535 (tpp) cc_final: 0.9099 (tmm) REVERT: B 51 ASP cc_start: 0.9143 (t0) cc_final: 0.8637 (t0) REVERT: B 55 MET cc_start: 0.9067 (mtm) cc_final: 0.8382 (mtm) REVERT: B 68 MET cc_start: 0.9035 (ttm) cc_final: 0.8589 (tpp) REVERT: B 79 GLU cc_start: 0.8183 (mp0) cc_final: 0.7979 (pm20) REVERT: B 84 HIS cc_start: 0.9383 (m90) cc_final: 0.9118 (m-70) REVERT: B 96 MET cc_start: 0.9168 (mmp) cc_final: 0.8826 (mpp) REVERT: B 103 ASP cc_start: 0.9217 (m-30) cc_final: 0.8869 (m-30) REVERT: B 118 MET cc_start: 0.8701 (mmm) cc_final: 0.8367 (ptm) REVERT: B 170 LYS cc_start: 0.9462 (tmmt) cc_final: 0.9125 (pttt) REVERT: C 5 ASN cc_start: 0.8087 (t0) cc_final: 0.7420 (p0) REVERT: C 52 LEU cc_start: 0.9589 (mp) cc_final: 0.9354 (mp) REVERT: C 68 MET cc_start: 0.9350 (mtp) cc_final: 0.9096 (mtt) REVERT: C 103 ASP cc_start: 0.8944 (m-30) cc_final: 0.8206 (t70) REVERT: C 104 ILE cc_start: 0.8846 (tt) cc_final: 0.8330 (pt) REVERT: C 130 TYR cc_start: 0.9326 (t80) cc_final: 0.9108 (t80) REVERT: C 140 LYS cc_start: 0.9439 (mtpp) cc_final: 0.9210 (mtpp) REVERT: C 158 LYS cc_start: 0.9218 (mmmt) cc_final: 0.8896 (mmmm) REVERT: C 167 ARG cc_start: 0.9395 (ptp90) cc_final: 0.9176 (ptp90) REVERT: C 168 PHE cc_start: 0.9450 (t80) cc_final: 0.9097 (t80) REVERT: C 182 LYS cc_start: 0.8537 (ptpt) cc_final: 0.8256 (ptpt) REVERT: D 10 MET cc_start: 0.6950 (mmp) cc_final: 0.6144 (tpp) REVERT: D 29 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7754 (mt-10) REVERT: D 53 ASN cc_start: 0.8599 (m-40) cc_final: 0.8165 (m110) REVERT: D 71 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8810 (pt0) REVERT: D 96 MET cc_start: 0.0917 (mmt) cc_final: 0.0634 (mpp) REVERT: D 100 ARG cc_start: 0.9018 (ttt180) cc_final: 0.8371 (ttm-80) REVERT: D 128 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8197 (tm-30) REVERT: D 129 ILE cc_start: 0.9166 (mt) cc_final: 0.8833 (tt) REVERT: D 132 ARG cc_start: 0.9284 (tmt-80) cc_final: 0.8838 (tpt90) REVERT: D 136 LEU cc_start: 0.9612 (tt) cc_final: 0.9238 (tt) REVERT: D 164 TYR cc_start: 0.8372 (t80) cc_final: 0.8122 (t80) REVERT: D 203 LYS cc_start: 0.9462 (mttt) cc_final: 0.9107 (mttt) REVERT: E 35 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8207 (tm-30) REVERT: E 68 MET cc_start: 0.8803 (mtp) cc_final: 0.8385 (tpp) REVERT: E 84 HIS cc_start: 0.9443 (m90) cc_final: 0.8798 (t-90) REVERT: E 96 MET cc_start: 0.8689 (mmp) cc_final: 0.7732 (mpp) REVERT: E 140 LYS cc_start: 0.9431 (mttt) cc_final: 0.9053 (tttt) REVERT: E 141 ILE cc_start: 0.9215 (mt) cc_final: 0.8925 (mt) REVERT: E 144 MET cc_start: 0.8512 (ppp) cc_final: 0.8063 (ppp) REVERT: F 52 LEU cc_start: 0.9698 (mp) cc_final: 0.9426 (mp) REVERT: F 68 MET cc_start: 0.9027 (mtt) cc_final: 0.8730 (mtt) REVERT: F 103 ASP cc_start: 0.8624 (m-30) cc_final: 0.8100 (t70) REVERT: F 104 ILE cc_start: 0.9039 (tt) cc_final: 0.8680 (pt) REVERT: F 118 MET cc_start: 0.8082 (mmp) cc_final: 0.7726 (mmm) REVERT: F 140 LYS cc_start: 0.9403 (mtpp) cc_final: 0.8865 (mtmm) REVERT: F 159 GLU cc_start: 0.8740 (pt0) cc_final: 0.7851 (mp0) REVERT: F 164 TYR cc_start: 0.8634 (t80) cc_final: 0.7670 (t80) REVERT: F 167 ARG cc_start: 0.9436 (ptp90) cc_final: 0.8504 (ptp90) REVERT: F 168 PHE cc_start: 0.9553 (t80) cc_final: 0.8951 (t80) REVERT: F 185 MET cc_start: 0.8865 (mmp) cc_final: 0.8586 (mmp) REVERT: F 190 LEU cc_start: 0.9158 (mt) cc_final: 0.8664 (mt) outliers start: 2 outliers final: 0 residues processed: 393 average time/residue: 0.2535 time to fit residues: 133.8126 Evaluate side-chains 315 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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: 0.6980 chunk 124 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 0.0470 chunk 88 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 99 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 overall best weight: 1.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 95 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.087985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.062189 restraints weight = 57607.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.065421 restraints weight = 34660.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067803 restraints weight = 24195.385| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.7341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10572 Z= 0.129 Angle : 0.696 8.686 14378 Z= 0.361 Chirality : 0.046 0.208 1604 Planarity : 0.006 0.077 1882 Dihedral : 4.240 22.185 1404 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: 0.32 (0.22), residues: 1310 helix: 0.68 (0.17), residues: 850 sheet: None (None), residues: 0 loop : -0.52 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 23 HIS 0.003 0.001 HIS D 62 PHE 0.015 0.002 PHE A 168 TYR 0.025 0.002 TYR D 130 ARG 0.008 0.001 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 577) hydrogen bonds : angle 4.26950 ( 1731) SS BOND : bond 0.00264 ( 6) SS BOND : angle 1.25632 ( 12) covalent geometry : bond 0.00298 (10566) covalent geometry : angle 0.69555 (14366) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4396.62 seconds wall clock time: 78 minutes 48.00 seconds (4728.00 seconds total)