Starting phenix.real_space_refine on Fri Feb 14 09:56:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6slu_10240/02_2025/6slu_10240.cif Found real_map, /net/cci-nas-00/data/ceres_data/6slu_10240/02_2025/6slu_10240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6slu_10240/02_2025/6slu_10240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6slu_10240/02_2025/6slu_10240.map" model { file = "/net/cci-nas-00/data/ceres_data/6slu_10240/02_2025/6slu_10240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6slu_10240/02_2025/6slu_10240.cif" } resolution = 4.7 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= 0.004 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-5592/modules/chem_data/mon_lib" Total number of atoms: 10336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "C" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "D" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "F" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Time building chain proxies: 8.12, per 1000 atoms: 0.79 Number of scatterers: 10336 At special positions: 0 Unit cell: (114.68, 113.46, 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: 2.45 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: 3.512A 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: 4.456A pdb=" N TRP A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.588A 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: 4.494A 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: 3.596A 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: 4.209A pdb=" N ALA B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 119 removed outlier: 3.587A 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: 4.746A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.774A 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: 3.955A 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: 3.624A pdb=" N GLN C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 31 removed outlier: 3.549A 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: 3.719A 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: 4.327A 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: 3.532A 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: 3.633A 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: 4.177A pdb=" N ALA E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.649A 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: 4.189A pdb=" N TRP E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 4.314A 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: 3.730A 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: 3.716A 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: 3.568A pdb=" N VAL A 3 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.602A 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: 4.466A 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: 3.795A pdb=" N VAL D 3 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.815A 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: 4.587A pdb=" N VAL F 3 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 4.479A 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: 2.55 Time building geometry restraints manager: 2.85 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: 3210 1.34 - 1.46: 1348 1.46 - 1.57: 5864 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 1.536 -0.063 1.40e-02 5.10e+03 1.99e+01 bond pdb=" N PRO A 34 " pdb=" CD PRO A 34 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.83e+01 bond pdb=" C SER A 33 " pdb=" N PRO A 34 " ideal model delta sigma weight residual 1.335 1.388 -0.054 1.28e-02 6.10e+03 1.77e+01 bond pdb=" N PRO D 34 " pdb=" CD PRO D 34 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.77e+01 bond pdb=" N PRO A 38 " pdb=" CD PRO A 38 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.72e+01 ... (remaining 10561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 14194 2.64 - 5.28: 155 5.28 - 7.92: 13 7.92 - 10.56: 0 10.56 - 13.20: 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 121.00 114.87 6.13 8.30e-01 1.45e+00 5.45e+01 angle pdb=" N GLU C 29 " pdb=" CA GLU C 29 " pdb=" C GLU C 29 " ideal model delta sigma weight residual 111.36 118.40 -7.04 1.09e+00 8.42e-01 4.18e+01 angle pdb=" N GLU B 29 " pdb=" CA GLU B 29 " pdb=" C GLU B 29 " ideal model delta sigma weight residual 111.36 118.22 -6.86 1.09e+00 8.42e-01 3.96e+01 angle pdb=" C ILE E 37 " pdb=" CA ILE E 37 " pdb=" CB ILE E 37 " ideal model delta sigma weight residual 114.35 107.80 6.55 1.06e+00 8.90e-01 3.82e+01 angle pdb=" O ILE D 37 " pdb=" C ILE D 37 " pdb=" N PRO D 38 " ideal model delta sigma weight residual 120.07 124.09 -4.02 7.10e-01 1.98e+00 3.21e+01 ... (remaining 14361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6209 17.92 - 35.84: 276 35.84 - 53.76: 31 53.76 - 71.68: 2 71.68 - 89.60: 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 -12.93 -73.07 1 1.00e+01 1.00e-02 6.80e+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 -117.96 31.96 1 1.00e+01 1.00e-02 1.46e+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 -130.68 8.08 0 2.50e+00 1.60e-01 1.04e+01 ... (remaining 6519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1223 0.044 - 0.088: 278 0.088 - 0.132: 81 0.132 - 0.177: 16 0.177 - 0.221: 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 0.22 2.00e-01 2.50e+01 1.22e+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 1.17e+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 7.00e-02 7.85e+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 " -0.039 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 2.07e-02 4.27e+00 pdb=" C GLU F 35 " -0.036 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 1.59e-02 2.53e+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: 3 2.14 - 2.83: 3257 2.83 - 3.52: 14581 3.52 - 4.21: 22149 4.21 - 4.90: 38246 Nonbonded interactions: 78236 Sorted by model distance: nonbonded pdb=" O THR D 58 " pdb=" OE2 GLU E 35 " model vdw 1.454 3.040 nonbonded pdb=" O PRO F 17 " pdb=" OD1 ASN F 21 " model vdw 2.029 3.040 nonbonded pdb=" OE1 GLU C 71 " pdb=" OG1 THR D 210 " model vdw 2.099 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 2.202 3.270 ... (remaining 78231 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.050 Find NCS groups from input model: 0.510 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: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10566 Z= 0.223 Angle : 0.639 13.203 14366 Z= 0.421 Chirality : 0.044 0.221 1604 Planarity : 0.004 0.070 1882 Dihedral : 9.227 89.598 4028 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.18 % Allowed : 5.04 % Favored : 94.78 % 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 0.001 TRP E 184 HIS 0.001 0.000 HIS E 62 PHE 0.012 0.001 PHE E 32 TYR 0.004 0.001 TYR E 130 ARG 0.002 0.000 ARG B 162 *********************** 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 641 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 639 time to evaluate : 1.168 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.9257 (tt0) cc_final: 0.8519 (tm-30) REVERT: A 68 MET cc_start: 0.9330 (mtp) cc_final: 0.8284 (mtt) REVERT: A 71 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 115 ILE cc_start: 0.9581 (mm) cc_final: 0.9374 (mm) REVERT: A 117 TRP cc_start: 0.6047 (m-10) cc_final: 0.5720 (m-10) REVERT: A 129 ILE cc_start: 0.9089 (mt) cc_final: 0.8530 (tt) REVERT: A 141 ILE cc_start: 0.9566 (mm) cc_final: 0.9324 (tp) REVERT: A 202 LEU cc_start: 0.9062 (mt) cc_final: 0.8815 (mm) REVERT: B 26 VAL cc_start: 0.9286 (p) cc_final: 0.9070 (m) REVERT: B 38 PRO cc_start: 0.9363 (Cg_exo) cc_final: 0.9057 (Cg_endo) REVERT: B 76 GLU cc_start: 0.9320 (tt0) cc_final: 0.9021 (tp30) REVERT: B 81 ASP cc_start: 0.9302 (t0) cc_final: 0.8508 (t0) REVERT: B 100 ARG cc_start: 0.8984 (ttp80) cc_final: 0.8626 (tpm170) REVERT: B 113 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9279 (mt-10) REVERT: B 114 GLN cc_start: 0.9731 (pt0) cc_final: 0.9073 (pt0) REVERT: B 128 GLU cc_start: 0.9465 (mp0) cc_final: 0.8944 (pp20) REVERT: B 129 ILE cc_start: 0.9656 (mm) cc_final: 0.9208 (tp) REVERT: B 141 ILE cc_start: 0.8869 (mt) cc_final: 0.8299 (mt) REVERT: B 144 MET cc_start: 0.8668 (tmm) cc_final: 0.8459 (ppp) REVERT: B 190 LEU cc_start: 0.9061 (mt) cc_final: 0.8771 (mt) REVERT: C 35 GLU cc_start: 0.8808 (pt0) cc_final: 0.8039 (tm-30) REVERT: C 53 ASN cc_start: 0.8562 (m-40) cc_final: 0.8257 (t0) REVERT: C 68 MET cc_start: 0.9550 (mtp) cc_final: 0.8817 (mtt) REVERT: C 75 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8194 (pp20) REVERT: C 76 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8756 (mm-30) REVERT: C 98 GLU cc_start: 0.9350 (mt-10) cc_final: 0.8736 (tm-30) REVERT: C 129 ILE cc_start: 0.9593 (mt) cc_final: 0.9386 (pt) REVERT: C 159 GLU cc_start: 0.8929 (mp0) cc_final: 0.8344 (pt0) REVERT: C 167 ARG cc_start: 0.8883 (ttt180) cc_final: 0.8622 (ptp-170) REVERT: D 16 SER cc_start: 0.9226 (t) cc_final: 0.8934 (p) REVERT: D 23 TRP cc_start: 0.9287 (t-100) cc_final: 0.8785 (t-100) REVERT: D 32 PHE cc_start: 0.7450 (m-80) cc_final: 0.7066 (m-80) REVERT: D 37 ILE cc_start: 0.9256 (mt) cc_final: 0.9046 (mt) REVERT: D 48 THR cc_start: 0.9592 (p) cc_final: 0.9382 (t) REVERT: D 50 GLN cc_start: 0.9237 (tt0) cc_final: 0.8852 (tm-30) REVERT: D 51 ASP cc_start: 0.9221 (m-30) cc_final: 0.8784 (m-30) REVERT: D 55 MET cc_start: 0.9222 (ttm) cc_final: 0.8982 (ttm) REVERT: D 68 MET cc_start: 0.9208 (mtp) cc_final: 0.8929 (mtp) REVERT: D 71 GLU cc_start: 0.9393 (mt-10) cc_final: 0.8863 (mt-10) REVERT: D 95 GLN cc_start: 0.6789 (tp40) cc_final: 0.6530 (pt0) REVERT: D 128 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8238 (tm-30) REVERT: D 129 ILE cc_start: 0.9091 (mt) cc_final: 0.8646 (tt) REVERT: D 138 LEU cc_start: 0.9493 (mt) cc_final: 0.9252 (tp) REVERT: D 152 ASP cc_start: 0.8092 (m-30) cc_final: 0.7870 (p0) REVERT: D 170 LYS cc_start: 0.9281 (tttt) cc_final: 0.9074 (tptt) REVERT: D 181 VAL cc_start: 0.8561 (p) cc_final: 0.8053 (p) REVERT: D 215 MET cc_start: 0.9067 (mtm) cc_final: 0.8466 (mtm) REVERT: E 28 GLU cc_start: 0.8953 (tt0) cc_final: 0.8546 (pt0) REVERT: E 95 GLN cc_start: 0.6651 (mm110) cc_final: 0.6361 (pt0) REVERT: E 100 ARG cc_start: 0.8933 (ttp80) cc_final: 0.8296 (tpp-160) REVERT: E 128 GLU cc_start: 0.9296 (mp0) cc_final: 0.8781 (pp20) REVERT: E 141 ILE cc_start: 0.8994 (mt) cc_final: 0.8447 (mt) REVERT: E 144 MET cc_start: 0.8239 (ppp) cc_final: 0.7839 (ppp) REVERT: E 161 PHE cc_start: 0.8011 (t80) cc_final: 0.7745 (t80) REVERT: F 52 LEU cc_start: 0.9832 (mp) cc_final: 0.9495 (mp) REVERT: F 68 MET cc_start: 0.9612 (mtp) cc_final: 0.9051 (mtt) REVERT: F 79 GLU cc_start: 0.9572 (tt0) cc_final: 0.9202 (tp30) REVERT: F 98 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8638 (tm-30) REVERT: F 129 ILE cc_start: 0.9596 (mt) cc_final: 0.9276 (pt) REVERT: F 141 ILE cc_start: 0.9231 (mt) cc_final: 0.9017 (mt) REVERT: F 142 VAL cc_start: 0.9263 (m) cc_final: 0.9014 (p) REVERT: F 158 LYS cc_start: 0.8542 (mmmt) cc_final: 0.8275 (mmmt) REVERT: F 159 GLU cc_start: 0.9066 (mp0) cc_final: 0.8569 (pt0) REVERT: F 164 TYR cc_start: 0.8638 (t80) cc_final: 0.7050 (t80) REVERT: F 185 MET cc_start: 0.8997 (ptp) cc_final: 0.8775 (ptp) REVERT: F 191 VAL cc_start: 0.8860 (p) cc_final: 0.8093 (p) REVERT: F 216 THR cc_start: 0.8760 (p) cc_final: 0.8251 (p) outliers start: 2 outliers final: 1 residues processed: 639 average time/residue: 0.2958 time to fit residues: 243.6076 Evaluate side-chains 392 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 391 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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: 0.0980 chunk 100 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 0.0980 chunk 62 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 overall best weight: 0.5120 ------------------------------------------------------------------------------- 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 87 HIS A 95 GLN B 21 ASN B 53 ASN B 95 GLN C 4 GLN C 5 ASN C 67 GLN C 192 GLN D 4 GLN D 9 GLN D 87 HIS D 112 GLN D 183 ASN E 13 GLN E 50 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN F 4 GLN F 139 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.098750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.070384 restraints weight = 71935.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.074321 restraints weight = 38339.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.077206 restraints weight = 25246.464| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10566 Z= 0.211 Angle : 0.634 7.546 14366 Z= 0.320 Chirality : 0.044 0.162 1604 Planarity : 0.005 0.047 1882 Dihedral : 3.378 15.737 1404 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.09 % Allowed : 2.83 % 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 (0.21), residues: 1310 helix: 0.31 (0.17), residues: 830 sheet: None (None), residues: 0 loop : -0.93 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 80 HIS 0.005 0.001 HIS E 62 PHE 0.022 0.002 PHE D 161 TYR 0.017 0.001 TYR E 145 ARG 0.005 0.001 ARG D 173 *********************** 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 508 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 507 time to evaluate : 1.090 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: A 10 MET cc_start: 0.5407 (tpt) cc_final: 0.5000 (mmm) REVERT: A 28 GLU cc_start: 0.8703 (tt0) cc_final: 0.8387 (pp20) REVERT: A 50 GLN cc_start: 0.9256 (tt0) cc_final: 0.8830 (tm-30) REVERT: A 51 ASP cc_start: 0.9295 (m-30) cc_final: 0.8846 (m-30) REVERT: A 68 MET cc_start: 0.9420 (mtp) cc_final: 0.8829 (mtt) REVERT: A 82 ARG cc_start: 0.9354 (ptm-80) cc_final: 0.9146 (ttp80) REVERT: A 129 ILE cc_start: 0.8855 (mt) cc_final: 0.8626 (tt) REVERT: A 141 ILE cc_start: 0.9621 (mm) cc_final: 0.9356 (tp) REVERT: A 144 MET cc_start: 0.9140 (tpp) cc_final: 0.8543 (tpp) REVERT: A 167 ARG cc_start: 0.9354 (mtm-85) cc_final: 0.8927 (ptt-90) REVERT: A 215 MET cc_start: 0.8519 (ptm) cc_final: 0.7886 (ptm) REVERT: B 10 MET cc_start: 0.6006 (tmm) cc_final: 0.5629 (tmm) REVERT: B 38 PRO cc_start: 0.9421 (Cg_exo) cc_final: 0.9207 (Cg_endo) REVERT: B 55 MET cc_start: 0.9544 (ttm) cc_final: 0.9098 (tpp) REVERT: B 96 MET cc_start: 0.4010 (mtm) cc_final: 0.3804 (mtt) REVERT: B 100 ARG cc_start: 0.8838 (ttp80) cc_final: 0.8607 (tpm170) REVERT: B 128 GLU cc_start: 0.9452 (mp0) cc_final: 0.8896 (pp20) REVERT: B 129 ILE cc_start: 0.9647 (mm) cc_final: 0.9006 (tp) REVERT: B 190 LEU cc_start: 0.8787 (mt) cc_final: 0.8267 (mt) REVERT: C 9 GLN cc_start: 0.8625 (tm-30) cc_final: 0.7997 (pm20) REVERT: C 25 LYS cc_start: 0.8690 (pttt) cc_final: 0.8256 (ttpt) REVERT: C 26 VAL cc_start: 0.8829 (p) cc_final: 0.8202 (p) REVERT: C 35 GLU cc_start: 0.8930 (pt0) cc_final: 0.8281 (tm-30) REVERT: C 53 ASN cc_start: 0.8569 (m-40) cc_final: 0.8350 (t0) REVERT: C 68 MET cc_start: 0.9456 (mtp) cc_final: 0.8727 (mtt) REVERT: C 98 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8744 (tm-30) REVERT: C 140 LYS cc_start: 0.9352 (mtmm) cc_final: 0.9119 (ptpp) REVERT: C 159 GLU cc_start: 0.8763 (mp0) cc_final: 0.8473 (pt0) REVERT: C 167 ARG cc_start: 0.8919 (ttt180) cc_final: 0.8680 (ptp90) REVERT: C 186 THR cc_start: 0.9033 (p) cc_final: 0.8741 (p) REVERT: C 215 MET cc_start: 0.8991 (ptp) cc_final: 0.8763 (ppp) REVERT: C 216 THR cc_start: 0.8643 (p) cc_final: 0.8018 (p) REVERT: D 16 SER cc_start: 0.9263 (t) cc_final: 0.8889 (p) REVERT: D 23 TRP cc_start: 0.9612 (t-100) cc_final: 0.9337 (t-100) REVERT: D 37 ILE cc_start: 0.9530 (mt) cc_final: 0.9203 (mt) REVERT: D 50 GLN cc_start: 0.9346 (tt0) cc_final: 0.8881 (tm-30) REVERT: D 51 ASP cc_start: 0.8708 (m-30) cc_final: 0.8100 (m-30) REVERT: D 55 MET cc_start: 0.9367 (ttm) cc_final: 0.9004 (ttp) REVERT: D 58 THR cc_start: 0.9283 (p) cc_final: 0.9069 (p) REVERT: D 63 GLN cc_start: 0.9170 (mp10) cc_final: 0.8846 (mp10) REVERT: D 67 GLN cc_start: 0.9435 (mm-40) cc_final: 0.9194 (mt0) REVERT: D 111 LEU cc_start: 0.9531 (tp) cc_final: 0.9260 (tp) REVERT: D 129 ILE cc_start: 0.9120 (mt) cc_final: 0.8648 (tt) REVERT: D 132 ARG cc_start: 0.9468 (mtp-110) cc_final: 0.9101 (ttp-110) REVERT: D 215 MET cc_start: 0.8859 (mtm) cc_final: 0.8377 (mtm) REVERT: E 28 GLU cc_start: 0.8878 (tt0) cc_final: 0.8476 (pt0) REVERT: E 30 LYS cc_start: 0.8922 (tppt) cc_final: 0.8313 (tptp) REVERT: E 55 MET cc_start: 0.9687 (ttm) cc_final: 0.9318 (tpp) REVERT: E 68 MET cc_start: 0.8970 (mtp) cc_final: 0.8751 (mtp) REVERT: E 100 ARG cc_start: 0.9146 (ttp80) cc_final: 0.8721 (tpp-160) REVERT: E 128 GLU cc_start: 0.9266 (mp0) cc_final: 0.8775 (tm-30) REVERT: E 129 ILE cc_start: 0.9516 (mm) cc_final: 0.8776 (mm) REVERT: E 141 ILE cc_start: 0.8817 (mt) cc_final: 0.8404 (mt) REVERT: E 190 LEU cc_start: 0.8870 (mt) cc_final: 0.8632 (mt) REVERT: F 13 GLN cc_start: 0.9384 (tp40) cc_final: 0.9170 (tp-100) REVERT: F 38 PRO cc_start: 0.9493 (Cg_exo) cc_final: 0.9274 (Cg_endo) REVERT: F 39 MET cc_start: 0.9238 (tpp) cc_final: 0.9024 (tpp) REVERT: F 68 MET cc_start: 0.9635 (mtp) cc_final: 0.8872 (mtt) REVERT: F 71 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8963 (tm-30) REVERT: F 75 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8524 (tm-30) REVERT: F 79 GLU cc_start: 0.9588 (tt0) cc_final: 0.9190 (tp30) REVERT: F 111 LEU cc_start: 0.9085 (tp) cc_final: 0.8258 (mp) REVERT: F 114 GLN cc_start: 0.8996 (mp-120) cc_final: 0.8127 (mp10) REVERT: F 117 TRP cc_start: 0.8315 (m-10) cc_final: 0.7523 (m-90) REVERT: F 129 ILE cc_start: 0.9659 (mt) cc_final: 0.9146 (mm) REVERT: F 132 ARG cc_start: 0.9451 (mtp-110) cc_final: 0.9097 (ptm-80) REVERT: F 158 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8207 (mmmt) REVERT: F 164 TYR cc_start: 0.8143 (t80) cc_final: 0.7084 (t80) REVERT: F 185 MET cc_start: 0.8878 (ptp) cc_final: 0.8656 (ptp) REVERT: F 190 LEU cc_start: 0.8854 (mt) cc_final: 0.8396 (mt) outliers start: 1 outliers final: 0 residues processed: 508 average time/residue: 0.2893 time to fit residues: 190.0845 Evaluate side-chains 385 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 0.0980 chunk 19 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 52 optimal weight: 0.0010 chunk 116 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 112 GLN E 13 GLN E 95 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 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 = 0.3576 r_free = 0.3576 target = 0.095792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.066326 restraints weight = 78053.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.070050 restraints weight = 41754.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.072777 restraints weight = 27783.497| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10566 Z= 0.208 Angle : 0.649 8.427 14366 Z= 0.330 Chirality : 0.045 0.159 1604 Planarity : 0.005 0.042 1882 Dihedral : 3.637 15.686 1404 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.18 % Allowed : 2.83 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1310 helix: 0.60 (0.18), residues: 818 sheet: None (None), residues: 0 loop : -0.70 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 23 HIS 0.003 0.001 HIS E 62 PHE 0.019 0.002 PHE B 40 TYR 0.009 0.001 TYR C 130 ARG 0.009 0.001 ARG E 167 *********************** 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 466 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 464 time to evaluate : 1.199 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 45 GLU cc_start: 0.9170 (tt0) cc_final: 0.8658 (pm20) REVERT: A 68 MET cc_start: 0.9424 (mtp) cc_final: 0.9091 (mtt) REVERT: A 76 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8226 (mt-10) REVERT: A 79 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8834 (tm-30) REVERT: A 128 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8162 (tm-30) REVERT: A 129 ILE cc_start: 0.9050 (mt) cc_final: 0.8642 (mt) REVERT: A 141 ILE cc_start: 0.9659 (mm) cc_final: 0.9381 (tp) REVERT: A 144 MET cc_start: 0.9096 (tpp) cc_final: 0.8512 (tpp) REVERT: A 167 ARG cc_start: 0.9318 (mtm-85) cc_final: 0.8820 (ptt-90) REVERT: A 171 THR cc_start: 0.9307 (p) cc_final: 0.8973 (p) REVERT: A 215 MET cc_start: 0.8440 (ptm) cc_final: 0.8012 (ptm) REVERT: B 10 MET cc_start: 0.6013 (tmm) cc_final: 0.5762 (tmm) REVERT: B 55 MET cc_start: 0.9606 (ttm) cc_final: 0.9093 (tpp) REVERT: B 68 MET cc_start: 0.9269 (mtt) cc_final: 0.8918 (mtt) REVERT: B 100 ARG cc_start: 0.8890 (ttp80) cc_final: 0.8608 (tpm170) REVERT: B 128 GLU cc_start: 0.9466 (mp0) cc_final: 0.8972 (pp20) REVERT: B 129 ILE cc_start: 0.9612 (mm) cc_final: 0.9391 (tp) REVERT: B 144 MET cc_start: 0.9048 (ppp) cc_final: 0.8744 (ppp) REVERT: B 190 LEU cc_start: 0.8909 (mt) cc_final: 0.8526 (mt) REVERT: C 9 GLN cc_start: 0.8406 (tm-30) cc_final: 0.7770 (pm20) REVERT: C 66 MET cc_start: 0.9202 (mpp) cc_final: 0.9001 (mpp) REVERT: C 68 MET cc_start: 0.9318 (mtp) cc_final: 0.8631 (mtt) REVERT: C 96 MET cc_start: 0.3161 (mpp) cc_final: 0.2469 (mpp) REVERT: C 140 LYS cc_start: 0.9426 (mtmm) cc_final: 0.9143 (ptpp) REVERT: C 159 GLU cc_start: 0.8841 (mp0) cc_final: 0.8401 (pt0) REVERT: C 167 ARG cc_start: 0.9042 (ttt180) cc_final: 0.8715 (ptp-170) REVERT: D 23 TRP cc_start: 0.9612 (t-100) cc_final: 0.9294 (t-100) REVERT: D 55 MET cc_start: 0.9400 (ttm) cc_final: 0.8959 (ttp) REVERT: D 68 MET cc_start: 0.9205 (mtt) cc_final: 0.8501 (mtt) REVERT: D 129 ILE cc_start: 0.9080 (mt) cc_final: 0.8780 (tt) REVERT: D 132 ARG cc_start: 0.9441 (mtp-110) cc_final: 0.9145 (ttm110) REVERT: D 165 VAL cc_start: 0.9689 (p) cc_final: 0.9432 (m) REVERT: D 185 MET cc_start: 0.9596 (ptp) cc_final: 0.9333 (mtt) REVERT: D 212 GLU cc_start: 0.9351 (pt0) cc_final: 0.8747 (pm20) REVERT: D 215 MET cc_start: 0.8777 (mtm) cc_final: 0.8153 (mtm) REVERT: E 10 MET cc_start: 0.5283 (tmm) cc_final: 0.5080 (tmm) REVERT: E 13 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8535 (pp30) REVERT: E 28 GLU cc_start: 0.8813 (tt0) cc_final: 0.8312 (pt0) REVERT: E 30 LYS cc_start: 0.8845 (tppt) cc_final: 0.8226 (tptp) REVERT: E 32 PHE cc_start: 0.7139 (m-80) cc_final: 0.6892 (m-80) REVERT: E 55 MET cc_start: 0.9625 (ttm) cc_final: 0.9207 (tpp) REVERT: E 66 MET cc_start: 0.9014 (mpp) cc_final: 0.8631 (mpp) REVERT: E 68 MET cc_start: 0.9081 (mtp) cc_final: 0.8487 (mtp) REVERT: E 71 GLU cc_start: 0.8142 (pp20) cc_final: 0.7937 (pp20) REVERT: E 100 ARG cc_start: 0.9127 (ttp80) cc_final: 0.8721 (tpp-160) REVERT: E 128 GLU cc_start: 0.9273 (mp0) cc_final: 0.8867 (tm-30) REVERT: E 129 ILE cc_start: 0.9477 (mm) cc_final: 0.8885 (mm) REVERT: E 131 LYS cc_start: 0.9670 (tttt) cc_final: 0.9452 (tptt) REVERT: E 132 ARG cc_start: 0.9346 (mtm110) cc_final: 0.9077 (mtm110) REVERT: E 141 ILE cc_start: 0.8620 (mt) cc_final: 0.8324 (mt) REVERT: E 144 MET cc_start: 0.7827 (ppp) cc_final: 0.7440 (ppp) REVERT: F 68 MET cc_start: 0.9229 (mtp) cc_final: 0.8838 (mtt) REVERT: F 75 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8430 (tm-30) REVERT: F 79 GLU cc_start: 0.9602 (tt0) cc_final: 0.9249 (tp30) REVERT: F 111 LEU cc_start: 0.8651 (tp) cc_final: 0.8445 (mm) REVERT: F 129 ILE cc_start: 0.9672 (mt) cc_final: 0.9195 (mm) REVERT: F 132 ARG cc_start: 0.9413 (mtp-110) cc_final: 0.9199 (ptm-80) REVERT: F 158 LYS cc_start: 0.8392 (mmmt) cc_final: 0.8123 (mmmt) REVERT: F 159 GLU cc_start: 0.7409 (pt0) cc_final: 0.6496 (pt0) REVERT: F 164 TYR cc_start: 0.8302 (t80) cc_final: 0.6771 (t80) REVERT: F 179 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8952 (tp-100) REVERT: F 185 MET cc_start: 0.8959 (ptp) cc_final: 0.8713 (ptp) REVERT: F 190 LEU cc_start: 0.8979 (mt) cc_final: 0.8522 (mt) outliers start: 2 outliers final: 1 residues processed: 466 average time/residue: 0.2948 time to fit residues: 177.3861 Evaluate side-chains 362 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 360 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 108 optimal weight: 0.0010 chunk 103 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN D 95 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN ** F 192 GLN ** 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 = 0.3545 r_free = 0.3545 target = 0.093883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.066071 restraints weight = 65608.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.069382 restraints weight = 37123.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.071784 restraints weight = 25351.071| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10566 Z= 0.215 Angle : 0.662 8.200 14366 Z= 0.340 Chirality : 0.045 0.181 1604 Planarity : 0.005 0.045 1882 Dihedral : 3.765 18.520 1404 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1310 helix: 0.56 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -0.53 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F 117 HIS 0.003 0.001 HIS C 62 PHE 0.020 0.002 PHE A 40 TYR 0.017 0.001 TYR B 145 ARG 0.010 0.001 ARG E 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 1.143 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: A 68 MET cc_start: 0.9439 (mtp) cc_final: 0.8985 (mtt) REVERT: A 98 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6918 (mt-10) REVERT: A 100 ARG cc_start: 0.8846 (ptm-80) cc_final: 0.8535 (ptm-80) REVERT: A 128 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8197 (tm-30) REVERT: A 129 ILE cc_start: 0.9172 (mt) cc_final: 0.8668 (mt) REVERT: A 141 ILE cc_start: 0.9667 (mm) cc_final: 0.9374 (tp) REVERT: A 144 MET cc_start: 0.9069 (tpp) cc_final: 0.8502 (tpp) REVERT: A 167 ARG cc_start: 0.9272 (mtm-85) cc_final: 0.8786 (ptt-90) REVERT: A 215 MET cc_start: 0.8235 (ptm) cc_final: 0.7971 (ptm) REVERT: B 10 MET cc_start: 0.6018 (tmm) cc_final: 0.5757 (tmm) REVERT: B 55 MET cc_start: 0.9643 (ttm) cc_final: 0.9113 (tpp) REVERT: B 100 ARG cc_start: 0.8901 (ttp80) cc_final: 0.8622 (tpm170) REVERT: B 128 GLU cc_start: 0.9433 (mp0) cc_final: 0.8979 (pp20) REVERT: B 129 ILE cc_start: 0.9605 (mm) cc_final: 0.9226 (tp) REVERT: B 141 ILE cc_start: 0.9054 (mt) cc_final: 0.8829 (mt) REVERT: B 144 MET cc_start: 0.8926 (ppp) cc_final: 0.8350 (ppp) REVERT: B 190 LEU cc_start: 0.9042 (mt) cc_final: 0.8720 (mt) REVERT: C 68 MET cc_start: 0.9394 (mtp) cc_final: 0.8705 (mtt) REVERT: C 71 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8694 (tm-30) REVERT: C 140 LYS cc_start: 0.9400 (mtmm) cc_final: 0.9138 (ptpp) REVERT: C 167 ARG cc_start: 0.9083 (ttt180) cc_final: 0.8706 (ptp90) REVERT: D 23 TRP cc_start: 0.9608 (t-100) cc_final: 0.9334 (t-100) REVERT: D 55 MET cc_start: 0.9449 (ttm) cc_final: 0.8998 (ttm) REVERT: D 96 MET cc_start: 0.7375 (tpt) cc_final: 0.7073 (tpp) REVERT: D 98 GLU cc_start: 0.6227 (mt-10) cc_final: 0.5945 (mt-10) REVERT: D 117 TRP cc_start: 0.7942 (m-10) cc_final: 0.7142 (m-90) REVERT: D 173 ARG cc_start: 0.9392 (ttm-80) cc_final: 0.9168 (ttp80) REVERT: D 185 MET cc_start: 0.9535 (ptp) cc_final: 0.9227 (mtt) REVERT: D 212 GLU cc_start: 0.9334 (pt0) cc_final: 0.8822 (pm20) REVERT: D 215 MET cc_start: 0.8844 (mtm) cc_final: 0.8296 (mtp) REVERT: E 10 MET cc_start: 0.5395 (tmm) cc_final: 0.5078 (tmm) REVERT: E 25 LYS cc_start: 0.9491 (tttp) cc_final: 0.9148 (ttmm) REVERT: E 28 GLU cc_start: 0.8798 (tt0) cc_final: 0.8361 (pt0) REVERT: E 30 LYS cc_start: 0.8877 (tppt) cc_final: 0.8239 (tptp) REVERT: E 55 MET cc_start: 0.9636 (ttm) cc_final: 0.9242 (tpp) REVERT: E 66 MET cc_start: 0.9054 (mpp) cc_final: 0.8574 (mpp) REVERT: E 100 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8723 (tpp-160) REVERT: E 128 GLU cc_start: 0.9310 (mp0) cc_final: 0.8834 (tm-30) REVERT: E 129 ILE cc_start: 0.9436 (mm) cc_final: 0.8759 (mm) REVERT: E 136 LEU cc_start: 0.9792 (tt) cc_final: 0.9416 (pp) REVERT: E 140 LYS cc_start: 0.9439 (mtpt) cc_final: 0.8861 (mttp) REVERT: E 141 ILE cc_start: 0.8660 (mt) cc_final: 0.8385 (mt) REVERT: E 144 MET cc_start: 0.7877 (ppp) cc_final: 0.7540 (ppp) REVERT: E 179 GLN cc_start: 0.9360 (pm20) cc_final: 0.8999 (pm20) REVERT: F 68 MET cc_start: 0.9383 (mtp) cc_final: 0.8557 (mtt) REVERT: F 79 GLU cc_start: 0.9577 (tt0) cc_final: 0.9257 (tp30) REVERT: F 85 PRO cc_start: 0.8243 (Cg_exo) cc_final: 0.7927 (Cg_endo) REVERT: F 103 ASP cc_start: 0.9171 (m-30) cc_final: 0.8867 (m-30) REVERT: F 111 LEU cc_start: 0.8730 (tp) cc_final: 0.8466 (mp) REVERT: F 129 ILE cc_start: 0.9678 (mt) cc_final: 0.9280 (mm) REVERT: F 132 ARG cc_start: 0.9518 (mtp-110) cc_final: 0.9115 (ptm-80) REVERT: F 143 ARG cc_start: 0.9171 (mmm-85) cc_final: 0.8963 (mmm-85) REVERT: F 164 TYR cc_start: 0.7726 (t80) cc_final: 0.6816 (t80) REVERT: F 168 PHE cc_start: 0.9379 (t80) cc_final: 0.9148 (t80) REVERT: F 179 GLN cc_start: 0.9221 (tp-100) cc_final: 0.9011 (tp-100) REVERT: F 185 MET cc_start: 0.9125 (ptp) cc_final: 0.8832 (ptp) REVERT: F 190 LEU cc_start: 0.9082 (mt) cc_final: 0.8724 (mt) outliers start: 1 outliers final: 0 residues processed: 433 average time/residue: 0.2944 time to fit residues: 163.8108 Evaluate side-chains 357 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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: 2.9990 chunk 82 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 0.0170 chunk 9 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 62 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.093488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.066043 restraints weight = 68709.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.069490 restraints weight = 37656.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.072004 restraints weight = 25309.962| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10566 Z= 0.198 Angle : 0.661 7.019 14366 Z= 0.337 Chirality : 0.045 0.146 1604 Planarity : 0.005 0.080 1882 Dihedral : 4.010 24.317 1404 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.09 % Allowed : 1.68 % Favored : 98.23 % 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: 0.34 (0.23), residues: 1310 helix: 0.69 (0.18), residues: 838 sheet: None (None), residues: 0 loop : -0.46 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 117 HIS 0.003 0.000 HIS B 62 PHE 0.018 0.002 PHE E 168 TYR 0.025 0.002 TYR E 169 ARG 0.012 0.001 ARG D 143 *********************** 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 438 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 437 time to evaluate : 1.147 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: A 68 MET cc_start: 0.9422 (mtp) cc_final: 0.8960 (mtt) REVERT: A 100 ARG cc_start: 0.8782 (ptm-80) cc_final: 0.8502 (ptm-80) REVERT: A 128 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 129 ILE cc_start: 0.9160 (mt) cc_final: 0.8702 (mt) REVERT: A 141 ILE cc_start: 0.9666 (mm) cc_final: 0.9393 (tp) REVERT: A 144 MET cc_start: 0.9050 (tpp) cc_final: 0.8511 (tpp) REVERT: A 150 ILE cc_start: 0.8494 (tp) cc_final: 0.7940 (tp) REVERT: A 163 ASP cc_start: 0.9109 (m-30) cc_final: 0.8357 (m-30) REVERT: A 167 ARG cc_start: 0.9229 (mtm-85) cc_final: 0.8726 (ptt-90) REVERT: A 171 THR cc_start: 0.9284 (p) cc_final: 0.8800 (p) REVERT: A 210 THR cc_start: 0.9345 (t) cc_final: 0.9099 (t) REVERT: A 215 MET cc_start: 0.8364 (ptm) cc_final: 0.7909 (ptm) REVERT: B 10 MET cc_start: 0.6206 (tmm) cc_final: 0.5854 (tmm) REVERT: B 66 MET cc_start: 0.9077 (mpp) cc_final: 0.8812 (mpp) REVERT: B 100 ARG cc_start: 0.8937 (ttp80) cc_final: 0.8649 (tpm170) REVERT: B 128 GLU cc_start: 0.9435 (mp0) cc_final: 0.8822 (pp20) REVERT: B 129 ILE cc_start: 0.9579 (mm) cc_final: 0.8577 (tp) REVERT: B 132 ARG cc_start: 0.9684 (ptp-110) cc_final: 0.9356 (mtm110) REVERT: B 141 ILE cc_start: 0.9092 (mt) cc_final: 0.8848 (mt) REVERT: B 144 MET cc_start: 0.8763 (ppp) cc_final: 0.8334 (ppp) REVERT: B 190 LEU cc_start: 0.9083 (mt) cc_final: 0.8797 (mt) REVERT: C 32 PHE cc_start: 0.8193 (m-80) cc_final: 0.7938 (m-80) REVERT: C 68 MET cc_start: 0.9449 (mtp) cc_final: 0.8640 (mtt) REVERT: C 71 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8743 (tm-30) REVERT: C 81 ASP cc_start: 0.9022 (m-30) cc_final: 0.8769 (m-30) REVERT: C 113 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8942 (tt0) REVERT: C 154 ARG cc_start: 0.7851 (tpp80) cc_final: 0.7609 (mmm-85) REVERT: C 167 ARG cc_start: 0.9100 (ttt180) cc_final: 0.8690 (ptp90) REVERT: D 23 TRP cc_start: 0.9613 (t-100) cc_final: 0.9246 (t-100) REVERT: D 55 MET cc_start: 0.9497 (ttm) cc_final: 0.8984 (ttp) REVERT: D 68 MET cc_start: 0.8697 (mtt) cc_final: 0.8128 (mtt) REVERT: D 70 LYS cc_start: 0.9526 (mtpt) cc_final: 0.9186 (ptpt) REVERT: D 71 GLU cc_start: 0.8761 (pp20) cc_final: 0.8459 (pp20) REVERT: D 96 MET cc_start: 0.7370 (tpt) cc_final: 0.7150 (tpp) REVERT: D 98 GLU cc_start: 0.6444 (mt-10) cc_final: 0.6131 (mt-10) REVERT: D 117 TRP cc_start: 0.8022 (m-10) cc_final: 0.7221 (m-90) REVERT: D 173 ARG cc_start: 0.9348 (ttm-80) cc_final: 0.9136 (ttp80) REVERT: D 185 MET cc_start: 0.9571 (ptp) cc_final: 0.9275 (mtt) REVERT: D 212 GLU cc_start: 0.9350 (pt0) cc_final: 0.8902 (pm20) REVERT: D 215 MET cc_start: 0.8939 (mtm) cc_final: 0.8280 (mtm) REVERT: E 10 MET cc_start: 0.5442 (tmm) cc_final: 0.5061 (tmm) REVERT: E 25 LYS cc_start: 0.9477 (tttp) cc_final: 0.9233 (ttmm) REVERT: E 28 GLU cc_start: 0.8823 (tt0) cc_final: 0.8329 (pt0) REVERT: E 30 LYS cc_start: 0.8892 (tppt) cc_final: 0.8357 (tptp) REVERT: E 55 MET cc_start: 0.9630 (ttm) cc_final: 0.9216 (tpp) REVERT: E 66 MET cc_start: 0.8970 (mpp) cc_final: 0.8575 (mpp) REVERT: E 100 ARG cc_start: 0.9115 (ttp80) cc_final: 0.8704 (tpp-160) REVERT: E 128 GLU cc_start: 0.9351 (mp0) cc_final: 0.8855 (tm-30) REVERT: E 129 ILE cc_start: 0.9441 (mm) cc_final: 0.8693 (mm) REVERT: E 132 ARG cc_start: 0.9351 (mtm110) cc_final: 0.8958 (mtm110) REVERT: E 141 ILE cc_start: 0.8720 (mt) cc_final: 0.8440 (mt) REVERT: E 144 MET cc_start: 0.7823 (ppp) cc_final: 0.7508 (ppp) REVERT: E 211 LEU cc_start: 0.9682 (pp) cc_final: 0.9379 (pp) REVERT: F 33 SER cc_start: 0.9092 (p) cc_final: 0.8885 (p) REVERT: F 68 MET cc_start: 0.9184 (mtp) cc_final: 0.8926 (mtp) REVERT: F 79 GLU cc_start: 0.9595 (tt0) cc_final: 0.9240 (tp30) REVERT: F 81 ASP cc_start: 0.8925 (m-30) cc_final: 0.8716 (m-30) REVERT: F 103 ASP cc_start: 0.9144 (m-30) cc_final: 0.8939 (m-30) REVERT: F 111 LEU cc_start: 0.8776 (tp) cc_final: 0.8575 (mp) REVERT: F 129 ILE cc_start: 0.9665 (mt) cc_final: 0.9314 (mm) REVERT: F 143 ARG cc_start: 0.9178 (mmm-85) cc_final: 0.8798 (mmm-85) REVERT: F 164 TYR cc_start: 0.7754 (t80) cc_final: 0.6768 (t80) REVERT: F 167 ARG cc_start: 0.8729 (ptt-90) cc_final: 0.8436 (ptt-90) REVERT: F 168 PHE cc_start: 0.9396 (t80) cc_final: 0.9169 (t80) REVERT: F 179 GLN cc_start: 0.9227 (tp-100) cc_final: 0.9007 (tp-100) REVERT: F 185 MET cc_start: 0.9145 (ptp) cc_final: 0.8869 (ptp) REVERT: F 190 LEU cc_start: 0.9061 (mt) cc_final: 0.8685 (mt) outliers start: 1 outliers final: 0 residues processed: 438 average time/residue: 0.3090 time to fit residues: 174.4331 Evaluate side-chains 370 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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: 9.9990 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.064162 restraints weight = 75720.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067656 restraints weight = 40305.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.070155 restraints weight = 26726.036| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.6255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10566 Z= 0.219 Angle : 0.662 7.098 14366 Z= 0.340 Chirality : 0.044 0.145 1604 Planarity : 0.005 0.097 1882 Dihedral : 4.044 23.247 1404 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % 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: 0.44 (0.23), residues: 1310 helix: 0.75 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.39 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 23 HIS 0.003 0.001 HIS D 12 PHE 0.021 0.002 PHE A 40 TYR 0.023 0.002 TYR E 169 ARG 0.011 0.001 ARG E 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 1.251 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: A 40 PHE cc_start: 0.9256 (t80) cc_final: 0.8973 (t80) REVERT: A 55 MET cc_start: 0.9410 (ttm) cc_final: 0.9107 (ttp) REVERT: A 68 MET cc_start: 0.9447 (mtp) cc_final: 0.9126 (mtt) REVERT: A 70 LYS cc_start: 0.9637 (mttt) cc_final: 0.9116 (ptpp) REVERT: A 96 MET cc_start: 0.6507 (tpt) cc_final: 0.6289 (tpp) REVERT: A 98 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7312 (mt-10) REVERT: A 100 ARG cc_start: 0.8892 (ptm-80) cc_final: 0.8643 (ptm-80) REVERT: A 128 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8105 (tm-30) REVERT: A 129 ILE cc_start: 0.9170 (mt) cc_final: 0.8739 (mt) REVERT: A 144 MET cc_start: 0.9135 (tpp) cc_final: 0.8658 (tpp) REVERT: A 163 ASP cc_start: 0.9089 (m-30) cc_final: 0.8777 (m-30) REVERT: A 167 ARG cc_start: 0.9175 (mtm-85) cc_final: 0.8678 (ptp90) REVERT: A 215 MET cc_start: 0.8470 (ptm) cc_final: 0.7976 (ptm) REVERT: B 10 MET cc_start: 0.6291 (tmm) cc_final: 0.5907 (tmm) REVERT: B 66 MET cc_start: 0.9105 (mpp) cc_final: 0.8746 (mpp) REVERT: B 100 ARG cc_start: 0.8944 (ttp80) cc_final: 0.8569 (tpm170) REVERT: B 128 GLU cc_start: 0.9468 (mp0) cc_final: 0.8851 (pp20) REVERT: B 131 LYS cc_start: 0.9690 (tptt) cc_final: 0.9481 (mmtt) REVERT: B 132 ARG cc_start: 0.9694 (ptp-110) cc_final: 0.9358 (mtm110) REVERT: B 141 ILE cc_start: 0.9068 (mt) cc_final: 0.8798 (mt) REVERT: B 144 MET cc_start: 0.8687 (ppp) cc_final: 0.8469 (ppp) REVERT: B 190 LEU cc_start: 0.9340 (mt) cc_final: 0.8938 (mt) REVERT: C 43 LEU cc_start: 0.9475 (tp) cc_final: 0.9234 (mm) REVERT: C 68 MET cc_start: 0.9452 (mtp) cc_final: 0.8694 (mtp) REVERT: C 71 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8696 (tm-30) REVERT: C 81 ASP cc_start: 0.9057 (m-30) cc_final: 0.8810 (m-30) REVERT: C 103 ASP cc_start: 0.9070 (m-30) cc_final: 0.8851 (m-30) REVERT: C 112 GLN cc_start: 0.9261 (mp10) cc_final: 0.9045 (mp10) REVERT: C 129 ILE cc_start: 0.9657 (pt) cc_final: 0.9430 (pt) REVERT: C 154 ARG cc_start: 0.8411 (tpp80) cc_final: 0.8183 (mmm-85) REVERT: C 167 ARG cc_start: 0.9108 (ttt180) cc_final: 0.8661 (ptp90) REVERT: C 215 MET cc_start: 0.8978 (ppp) cc_final: 0.8758 (ppp) REVERT: D 10 MET cc_start: 0.5065 (mmm) cc_final: 0.4823 (mmm) REVERT: D 55 MET cc_start: 0.9487 (ttm) cc_final: 0.8977 (ttm) REVERT: D 68 MET cc_start: 0.8743 (mtt) cc_final: 0.8256 (mtt) REVERT: D 70 LYS cc_start: 0.9523 (mtpt) cc_final: 0.9156 (ptpt) REVERT: D 71 GLU cc_start: 0.8808 (pp20) cc_final: 0.8434 (pp20) REVERT: D 96 MET cc_start: 0.7600 (tpt) cc_final: 0.7386 (tpp) REVERT: D 98 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6242 (mt-10) REVERT: D 117 TRP cc_start: 0.8056 (m-10) cc_final: 0.7162 (m-90) REVERT: D 132 ARG cc_start: 0.9526 (mtp-110) cc_final: 0.9057 (ttm110) REVERT: D 185 MET cc_start: 0.9569 (ptp) cc_final: 0.9217 (mtt) REVERT: D 212 GLU cc_start: 0.9311 (pt0) cc_final: 0.8602 (pm20) REVERT: D 215 MET cc_start: 0.8900 (mtm) cc_final: 0.7868 (mtm) REVERT: E 10 MET cc_start: 0.5537 (tmm) cc_final: 0.5092 (tmm) REVERT: E 25 LYS cc_start: 0.9459 (tttp) cc_final: 0.9116 (ttmm) REVERT: E 28 GLU cc_start: 0.8792 (tt0) cc_final: 0.8233 (pt0) REVERT: E 30 LYS cc_start: 0.8865 (tppt) cc_final: 0.8336 (tptp) REVERT: E 32 PHE cc_start: 0.6617 (m-80) cc_final: 0.6336 (m-10) REVERT: E 55 MET cc_start: 0.9653 (ttm) cc_final: 0.9293 (tpp) REVERT: E 66 MET cc_start: 0.8945 (mpp) cc_final: 0.8512 (mpp) REVERT: E 68 MET cc_start: 0.9064 (mtp) cc_final: 0.8439 (mtp) REVERT: E 71 GLU cc_start: 0.8569 (pp20) cc_final: 0.8335 (pp20) REVERT: E 72 THR cc_start: 0.9045 (p) cc_final: 0.8410 (p) REVERT: E 100 ARG cc_start: 0.9115 (ttp80) cc_final: 0.8708 (tpp-160) REVERT: E 128 GLU cc_start: 0.9373 (mp0) cc_final: 0.8862 (tm-30) REVERT: E 129 ILE cc_start: 0.9446 (mm) cc_final: 0.8796 (mm) REVERT: E 132 ARG cc_start: 0.9350 (mtm110) cc_final: 0.9057 (mtm110) REVERT: E 141 ILE cc_start: 0.8848 (mt) cc_final: 0.8602 (mt) REVERT: E 144 MET cc_start: 0.8128 (ppp) cc_final: 0.7807 (ppp) REVERT: F 68 MET cc_start: 0.9363 (mtp) cc_final: 0.8539 (mtt) REVERT: F 70 LYS cc_start: 0.9637 (mmmm) cc_final: 0.9352 (mmmm) REVERT: F 71 GLU cc_start: 0.8715 (pp20) cc_final: 0.8388 (pp20) REVERT: F 79 GLU cc_start: 0.9617 (tt0) cc_final: 0.9261 (tp30) REVERT: F 81 ASP cc_start: 0.8926 (m-30) cc_final: 0.8706 (m-30) REVERT: F 129 ILE cc_start: 0.9670 (mt) cc_final: 0.9439 (mm) REVERT: F 132 ARG cc_start: 0.9621 (mtp-110) cc_final: 0.9262 (ptm-80) REVERT: F 143 ARG cc_start: 0.9207 (mmm-85) cc_final: 0.8773 (mmm-85) REVERT: F 164 TYR cc_start: 0.7868 (t80) cc_final: 0.6740 (t80) REVERT: F 168 PHE cc_start: 0.9432 (t80) cc_final: 0.9226 (t80) REVERT: F 179 GLN cc_start: 0.9228 (tp-100) cc_final: 0.9002 (tp-100) REVERT: F 185 MET cc_start: 0.9155 (ptp) cc_final: 0.8866 (ptp) REVERT: F 190 LEU cc_start: 0.9085 (mt) cc_final: 0.8741 (mt) REVERT: F 215 MET cc_start: 0.9294 (ppp) cc_final: 0.9056 (ppp) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.2988 time to fit residues: 162.0529 Evaluate side-chains 356 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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: 5.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.090080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.063064 restraints weight = 74698.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.066544 restraints weight = 39978.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.069050 restraints weight = 26364.631| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10566 Z= 0.249 Angle : 0.688 6.725 14366 Z= 0.355 Chirality : 0.045 0.187 1604 Planarity : 0.005 0.081 1882 Dihedral : 4.179 21.961 1404 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.09 % Allowed : 1.42 % Favored : 98.50 % 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: 0.40 (0.23), residues: 1310 helix: 0.73 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.42 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 23 HIS 0.004 0.001 HIS A 12 PHE 0.020 0.003 PHE E 168 TYR 0.022 0.002 TYR E 169 ARG 0.012 0.001 ARG E 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 1.216 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 10 MET cc_start: 0.5541 (mmm) cc_final: 0.5247 (mmm) REVERT: A 55 MET cc_start: 0.9440 (ttm) cc_final: 0.9190 (ttp) REVERT: A 68 MET cc_start: 0.9400 (mtp) cc_final: 0.9097 (mtt) REVERT: A 96 MET cc_start: 0.6905 (tpt) cc_final: 0.6584 (tpp) REVERT: A 98 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7430 (mt-10) REVERT: A 128 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8236 (tm-30) REVERT: A 129 ILE cc_start: 0.9166 (mt) cc_final: 0.8737 (mt) REVERT: A 144 MET cc_start: 0.9199 (tpp) cc_final: 0.8725 (tpp) REVERT: A 163 ASP cc_start: 0.9076 (m-30) cc_final: 0.8245 (m-30) REVERT: A 167 ARG cc_start: 0.9028 (mtm-85) cc_final: 0.8397 (ptt-90) REVERT: A 214 MET cc_start: 0.9169 (ptp) cc_final: 0.8933 (ptp) REVERT: A 215 MET cc_start: 0.8508 (ptm) cc_final: 0.8308 (ptm) REVERT: B 10 MET cc_start: 0.6307 (tmm) cc_final: 0.5919 (tmm) REVERT: B 55 MET cc_start: 0.9608 (ttm) cc_final: 0.9218 (ttm) REVERT: B 66 MET cc_start: 0.9117 (mpp) cc_final: 0.8760 (mpp) REVERT: B 68 MET cc_start: 0.9205 (mtp) cc_final: 0.8727 (mtp) REVERT: B 72 THR cc_start: 0.9127 (p) cc_final: 0.8604 (p) REVERT: B 81 ASP cc_start: 0.9146 (m-30) cc_final: 0.8574 (m-30) REVERT: B 100 ARG cc_start: 0.8930 (ttp80) cc_final: 0.8647 (tpm170) REVERT: B 128 GLU cc_start: 0.9441 (mp0) cc_final: 0.9035 (mp0) REVERT: B 129 ILE cc_start: 0.9576 (mm) cc_final: 0.9244 (tp) REVERT: B 132 ARG cc_start: 0.9686 (ptp-110) cc_final: 0.9469 (ptp-110) REVERT: B 141 ILE cc_start: 0.9201 (mt) cc_final: 0.8822 (mt) REVERT: B 144 MET cc_start: 0.8479 (ppp) cc_final: 0.8213 (ppp) REVERT: B 190 LEU cc_start: 0.9298 (mt) cc_final: 0.9031 (mt) REVERT: C 43 LEU cc_start: 0.9439 (tp) cc_final: 0.9186 (mm) REVERT: C 71 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8760 (tm-30) REVERT: C 75 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8358 (tm-30) REVERT: C 81 ASP cc_start: 0.9086 (m-30) cc_final: 0.8804 (m-30) REVERT: C 97 ARG cc_start: 0.8809 (ttp-110) cc_final: 0.8552 (ptt90) REVERT: C 103 ASP cc_start: 0.9077 (m-30) cc_final: 0.8816 (m-30) REVERT: C 129 ILE cc_start: 0.9671 (pt) cc_final: 0.9397 (pt) REVERT: C 140 LYS cc_start: 0.9482 (mtmm) cc_final: 0.8911 (ttpp) REVERT: C 167 ARG cc_start: 0.9167 (ttt180) cc_final: 0.8696 (ptp90) REVERT: C 185 MET cc_start: 0.9041 (ptp) cc_final: 0.8586 (ptp) REVERT: C 215 MET cc_start: 0.9007 (ppp) cc_final: 0.8747 (ppp) REVERT: C 216 THR cc_start: 0.8495 (p) cc_final: 0.8233 (p) REVERT: D 55 MET cc_start: 0.9354 (ttm) cc_final: 0.9136 (ttm) REVERT: D 68 MET cc_start: 0.8796 (mtt) cc_final: 0.8189 (mtt) REVERT: D 70 LYS cc_start: 0.9518 (mtpt) cc_final: 0.9126 (ptpp) REVERT: D 71 GLU cc_start: 0.8846 (pp20) cc_final: 0.8511 (pp20) REVERT: D 98 GLU cc_start: 0.6583 (mt-10) cc_final: 0.6270 (mt-10) REVERT: D 117 TRP cc_start: 0.8066 (m-10) cc_final: 0.6990 (m-90) REVERT: D 129 ILE cc_start: 0.9209 (mt) cc_final: 0.8819 (mm) REVERT: D 132 ARG cc_start: 0.9418 (mtp-110) cc_final: 0.9164 (ttm110) REVERT: D 185 MET cc_start: 0.9515 (ptp) cc_final: 0.9133 (mtt) REVERT: D 212 GLU cc_start: 0.9313 (pt0) cc_final: 0.8845 (pm20) REVERT: D 214 MET cc_start: 0.9296 (mtm) cc_final: 0.9078 (mtt) REVERT: E 10 MET cc_start: 0.5653 (tmm) cc_final: 0.5160 (tmm) REVERT: E 25 LYS cc_start: 0.9461 (tttp) cc_final: 0.9205 (ttmm) REVERT: E 28 GLU cc_start: 0.8731 (tt0) cc_final: 0.8287 (pt0) REVERT: E 30 LYS cc_start: 0.8913 (tppt) cc_final: 0.8373 (tptp) REVERT: E 32 PHE cc_start: 0.6780 (m-80) cc_final: 0.6510 (m-10) REVERT: E 66 MET cc_start: 0.8896 (mpp) cc_final: 0.8450 (mpp) REVERT: E 68 MET cc_start: 0.9051 (mtp) cc_final: 0.8429 (mtp) REVERT: E 71 GLU cc_start: 0.8656 (pp20) cc_final: 0.8421 (pp20) REVERT: E 72 THR cc_start: 0.9035 (p) cc_final: 0.8381 (p) REVERT: E 100 ARG cc_start: 0.9147 (ttp80) cc_final: 0.8705 (tpp-160) REVERT: E 128 GLU cc_start: 0.9345 (mp0) cc_final: 0.8860 (tm-30) REVERT: E 129 ILE cc_start: 0.9451 (mm) cc_final: 0.8784 (mm) REVERT: E 132 ARG cc_start: 0.9380 (mtm110) cc_final: 0.9074 (mtm110) REVERT: E 141 ILE cc_start: 0.8896 (mt) cc_final: 0.8621 (mt) REVERT: E 144 MET cc_start: 0.8172 (ppp) cc_final: 0.7868 (ppp) REVERT: F 39 MET cc_start: 0.9243 (tpp) cc_final: 0.8997 (tpp) REVERT: F 68 MET cc_start: 0.9101 (mtp) cc_final: 0.8748 (mtt) REVERT: F 70 LYS cc_start: 0.9624 (mmmm) cc_final: 0.9342 (mmmm) REVERT: F 79 GLU cc_start: 0.9619 (tt0) cc_final: 0.9272 (tp30) REVERT: F 81 ASP cc_start: 0.8988 (m-30) cc_final: 0.8730 (m-30) REVERT: F 143 ARG cc_start: 0.9141 (mmm-85) cc_final: 0.8825 (mmm-85) REVERT: F 164 TYR cc_start: 0.7819 (t80) cc_final: 0.6920 (t80) REVERT: F 167 ARG cc_start: 0.8988 (ptt-90) cc_final: 0.8538 (ptt-90) REVERT: F 168 PHE cc_start: 0.9531 (t80) cc_final: 0.9218 (t80) REVERT: F 179 GLN cc_start: 0.9262 (tp-100) cc_final: 0.9023 (tp-100) REVERT: F 185 MET cc_start: 0.9173 (ptp) cc_final: 0.8890 (ptp) REVERT: F 190 LEU cc_start: 0.9019 (mt) cc_final: 0.8641 (mt) outliers start: 1 outliers final: 1 residues processed: 413 average time/residue: 0.2963 time to fit residues: 157.3736 Evaluate side-chains 347 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 34 optimal weight: 0.0170 chunk 41 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.088957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.063285 restraints weight = 67077.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.066517 restraints weight = 37099.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.068846 restraints weight = 25016.554| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.6980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10566 Z= 0.245 Angle : 0.696 8.597 14366 Z= 0.359 Chirality : 0.046 0.209 1604 Planarity : 0.005 0.061 1882 Dihedral : 4.254 21.394 1404 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % 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: 0.39 (0.23), residues: 1310 helix: 0.75 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.47 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 133 HIS 0.003 0.001 HIS E 12 PHE 0.021 0.002 PHE B 40 TYR 0.015 0.002 TYR B 169 ARG 0.011 0.001 ARG A 82 *********************** 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 423 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 1.165 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 55 MET cc_start: 0.9478 (ttm) cc_final: 0.9259 (ttp) REVERT: A 68 MET cc_start: 0.9408 (mtp) cc_final: 0.9106 (mtt) REVERT: A 96 MET cc_start: 0.7274 (tpt) cc_final: 0.7021 (tpp) REVERT: A 98 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7482 (mt-10) REVERT: A 128 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 129 ILE cc_start: 0.9158 (mt) cc_final: 0.8733 (mt) REVERT: A 144 MET cc_start: 0.9167 (tpp) cc_final: 0.8666 (tpp) REVERT: A 167 ARG cc_start: 0.9010 (mtm-85) cc_final: 0.8572 (mtm180) REVERT: A 214 MET cc_start: 0.9211 (ptp) cc_final: 0.8935 (ptp) REVERT: B 10 MET cc_start: 0.6367 (tmm) cc_final: 0.5816 (tmm) REVERT: B 58 THR cc_start: 0.9394 (p) cc_final: 0.9014 (p) REVERT: B 72 THR cc_start: 0.9133 (p) cc_final: 0.8845 (p) REVERT: B 82 ARG cc_start: 0.8624 (tmm160) cc_final: 0.8133 (ttp80) REVERT: B 100 ARG cc_start: 0.8956 (ttp80) cc_final: 0.8678 (mmp80) REVERT: B 128 GLU cc_start: 0.9487 (mp0) cc_final: 0.9138 (mp0) REVERT: B 129 ILE cc_start: 0.9557 (mm) cc_final: 0.9249 (tp) REVERT: C 68 MET cc_start: 0.9522 (mtp) cc_final: 0.8944 (mtt) REVERT: C 81 ASP cc_start: 0.9108 (m-30) cc_final: 0.8830 (m-30) REVERT: C 97 ARG cc_start: 0.8862 (ttp-110) cc_final: 0.8506 (ptt90) REVERT: C 103 ASP cc_start: 0.9125 (m-30) cc_final: 0.8915 (m-30) REVERT: C 129 ILE cc_start: 0.9660 (pt) cc_final: 0.9415 (pt) REVERT: C 134 ILE cc_start: 0.9574 (mm) cc_final: 0.9353 (mm) REVERT: C 154 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8230 (mmm-85) REVERT: C 167 ARG cc_start: 0.9159 (ttt180) cc_final: 0.8737 (ptp90) REVERT: C 185 MET cc_start: 0.9032 (ptp) cc_final: 0.8632 (ptp) REVERT: C 215 MET cc_start: 0.9020 (ppp) cc_final: 0.8737 (ppp) REVERT: C 216 THR cc_start: 0.8443 (p) cc_final: 0.8129 (p) REVERT: D 55 MET cc_start: 0.9493 (ttm) cc_final: 0.9263 (ttp) REVERT: D 68 MET cc_start: 0.8774 (mtt) cc_final: 0.8165 (mtt) REVERT: D 71 GLU cc_start: 0.8912 (pp20) cc_final: 0.8500 (pp20) REVERT: D 98 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6387 (mt-10) REVERT: D 117 TRP cc_start: 0.7982 (m-10) cc_final: 0.6943 (m-90) REVERT: D 132 ARG cc_start: 0.9442 (mtp-110) cc_final: 0.9044 (ttm110) REVERT: D 173 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8368 (ttp80) REVERT: D 185 MET cc_start: 0.9492 (ptp) cc_final: 0.9074 (mtt) REVERT: D 187 GLU cc_start: 0.9006 (pt0) cc_final: 0.8624 (pp20) REVERT: D 215 MET cc_start: 0.8847 (mtm) cc_final: 0.8026 (mtm) REVERT: E 10 MET cc_start: 0.5678 (tmm) cc_final: 0.5009 (tmm) REVERT: E 25 LYS cc_start: 0.9435 (tttp) cc_final: 0.9201 (ttmm) REVERT: E 28 GLU cc_start: 0.8700 (tt0) cc_final: 0.8227 (pt0) REVERT: E 30 LYS cc_start: 0.8842 (tppt) cc_final: 0.8369 (tptp) REVERT: E 32 PHE cc_start: 0.6773 (m-80) cc_final: 0.6479 (m-10) REVERT: E 66 MET cc_start: 0.8997 (mpp) cc_final: 0.8471 (mpp) REVERT: E 68 MET cc_start: 0.9065 (mtp) cc_final: 0.8482 (mtp) REVERT: E 100 ARG cc_start: 0.9132 (ttp80) cc_final: 0.8698 (tpp-160) REVERT: E 128 GLU cc_start: 0.9360 (mp0) cc_final: 0.8843 (tm-30) REVERT: E 129 ILE cc_start: 0.9476 (mm) cc_final: 0.8790 (mm) REVERT: E 132 ARG cc_start: 0.9357 (mtm110) cc_final: 0.8905 (mtm110) REVERT: E 141 ILE cc_start: 0.8917 (mt) cc_final: 0.8646 (mt) REVERT: E 144 MET cc_start: 0.8146 (ppp) cc_final: 0.7864 (ppp) REVERT: F 39 MET cc_start: 0.9243 (tpp) cc_final: 0.9022 (tpp) REVERT: F 68 MET cc_start: 0.9088 (mtp) cc_final: 0.8838 (mtt) REVERT: F 79 GLU cc_start: 0.9605 (tt0) cc_final: 0.9279 (tp30) REVERT: F 81 ASP cc_start: 0.8946 (m-30) cc_final: 0.8705 (m-30) REVERT: F 97 ARG cc_start: 0.8774 (ttp-110) cc_final: 0.8021 (ptt-90) REVERT: F 103 ASP cc_start: 0.9016 (m-30) cc_final: 0.8702 (m-30) REVERT: F 111 LEU cc_start: 0.9316 (tp) cc_final: 0.9068 (tp) REVERT: F 129 ILE cc_start: 0.9627 (pt) cc_final: 0.9354 (pt) REVERT: F 132 ARG cc_start: 0.9662 (mtp-110) cc_final: 0.9351 (mtm110) REVERT: F 143 ARG cc_start: 0.9127 (mmm-85) cc_final: 0.8793 (mmm-85) REVERT: F 158 LYS cc_start: 0.8201 (mmpt) cc_final: 0.7997 (mmmt) REVERT: F 164 TYR cc_start: 0.7914 (t80) cc_final: 0.6803 (t80) REVERT: F 167 ARG cc_start: 0.8965 (ptt-90) cc_final: 0.8478 (ptt-90) REVERT: F 168 PHE cc_start: 0.9500 (t80) cc_final: 0.9088 (t80) REVERT: F 179 GLN cc_start: 0.9254 (tp-100) cc_final: 0.8983 (tp-100) REVERT: F 185 MET cc_start: 0.9198 (ptp) cc_final: 0.8959 (ptp) REVERT: F 190 LEU cc_start: 0.8916 (mt) cc_final: 0.8578 (mt) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.2975 time to fit residues: 161.7083 Evaluate side-chains 341 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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: 6.9990 chunk 3 optimal weight: 0.2980 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 113 optimal weight: 0.0670 chunk 108 optimal weight: 30.0000 chunk 129 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.091182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.063041 restraints weight = 90444.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.066863 restraints weight = 44160.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.069611 restraints weight = 28102.151| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.7027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10566 Z= 0.216 Angle : 0.716 7.853 14366 Z= 0.364 Chirality : 0.047 0.181 1604 Planarity : 0.005 0.055 1882 Dihedral : 4.167 20.168 1404 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.23), residues: 1310 helix: 0.73 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.41 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 23 HIS 0.003 0.000 HIS E 62 PHE 0.023 0.002 PHE D 40 TYR 0.013 0.002 TYR B 145 ARG 0.010 0.001 ARG A 82 *********************** 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 437 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.9282 (tt0) cc_final: 0.8599 (pm20) REVERT: A 55 MET cc_start: 0.9463 (ttm) cc_final: 0.9261 (ttp) REVERT: A 68 MET cc_start: 0.9387 (mtp) cc_final: 0.9085 (mtt) REVERT: A 96 MET cc_start: 0.7279 (tpt) cc_final: 0.7067 (tpp) REVERT: A 98 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7568 (mt-10) REVERT: A 128 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8249 (tm-30) REVERT: A 129 ILE cc_start: 0.9142 (mt) cc_final: 0.8711 (mt) REVERT: A 143 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.8045 (ttm110) REVERT: A 163 ASP cc_start: 0.8985 (m-30) cc_final: 0.8349 (m-30) REVERT: A 167 ARG cc_start: 0.9048 (mtm-85) cc_final: 0.8456 (ptt-90) REVERT: A 214 MET cc_start: 0.9150 (ptp) cc_final: 0.8940 (ptp) REVERT: B 2 ILE cc_start: 0.8454 (tp) cc_final: 0.8197 (mp) REVERT: B 10 MET cc_start: 0.6299 (tmm) cc_final: 0.5796 (tmm) REVERT: B 32 PHE cc_start: 0.6140 (m-80) cc_final: 0.5682 (m-80) REVERT: B 68 MET cc_start: 0.8952 (mtp) cc_final: 0.8447 (mtp) REVERT: B 72 THR cc_start: 0.9245 (p) cc_final: 0.8511 (p) REVERT: B 81 ASP cc_start: 0.9186 (m-30) cc_final: 0.8040 (m-30) REVERT: B 100 ARG cc_start: 0.9025 (ttp80) cc_final: 0.8557 (tpp-160) REVERT: B 128 GLU cc_start: 0.9463 (mp0) cc_final: 0.9081 (mp0) REVERT: B 129 ILE cc_start: 0.9539 (mm) cc_final: 0.9177 (tp) REVERT: B 132 ARG cc_start: 0.9638 (ptp-110) cc_final: 0.9432 (ptp-110) REVERT: B 141 ILE cc_start: 0.9326 (mt) cc_final: 0.8947 (mt) REVERT: C 50 GLN cc_start: 0.8773 (mp10) cc_final: 0.8487 (mp10) REVERT: C 81 ASP cc_start: 0.9032 (m-30) cc_final: 0.8789 (m-30) REVERT: C 97 ARG cc_start: 0.8877 (ttp-110) cc_final: 0.8516 (ptt90) REVERT: C 103 ASP cc_start: 0.9065 (m-30) cc_final: 0.8811 (m-30) REVERT: C 129 ILE cc_start: 0.9659 (pt) cc_final: 0.9452 (pt) REVERT: C 134 ILE cc_start: 0.9538 (mm) cc_final: 0.9308 (mm) REVERT: C 154 ARG cc_start: 0.8382 (tpp80) cc_final: 0.8130 (mmm-85) REVERT: C 167 ARG cc_start: 0.9105 (ttt180) cc_final: 0.8663 (ptp90) REVERT: C 185 MET cc_start: 0.9033 (ptp) cc_final: 0.8622 (ptp) REVERT: D 68 MET cc_start: 0.8748 (mtt) cc_final: 0.8121 (mtt) REVERT: D 70 LYS cc_start: 0.9522 (mtpt) cc_final: 0.9123 (ptpt) REVERT: D 71 GLU cc_start: 0.8876 (pp20) cc_final: 0.8451 (pp20) REVERT: D 98 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6546 (mt-10) REVERT: D 111 LEU cc_start: 0.9596 (tp) cc_final: 0.9336 (tp) REVERT: D 117 TRP cc_start: 0.8003 (m-10) cc_final: 0.7212 (m-90) REVERT: D 126 VAL cc_start: 0.8218 (t) cc_final: 0.7834 (t) REVERT: D 129 ILE cc_start: 0.9138 (tt) cc_final: 0.8870 (pt) REVERT: D 180 GLU cc_start: 0.8802 (pp20) cc_final: 0.8328 (pp20) REVERT: D 185 MET cc_start: 0.9506 (ptp) cc_final: 0.9144 (mtt) REVERT: D 187 GLU cc_start: 0.9091 (pt0) cc_final: 0.8714 (pp20) REVERT: D 215 MET cc_start: 0.8936 (mtm) cc_final: 0.8197 (mtm) REVERT: E 10 MET cc_start: 0.5794 (tmm) cc_final: 0.5113 (tmm) REVERT: E 28 GLU cc_start: 0.8739 (tt0) cc_final: 0.8269 (pt0) REVERT: E 30 LYS cc_start: 0.8829 (tppt) cc_final: 0.8325 (tptp) REVERT: E 32 PHE cc_start: 0.6434 (m-80) cc_final: 0.6208 (m-10) REVERT: E 66 MET cc_start: 0.9043 (mpp) cc_final: 0.8594 (mpp) REVERT: E 68 MET cc_start: 0.8953 (mtp) cc_final: 0.8502 (mtp) REVERT: E 71 GLU cc_start: 0.8644 (pp20) cc_final: 0.8385 (pp20) REVERT: E 72 THR cc_start: 0.9128 (p) cc_final: 0.8670 (p) REVERT: E 74 ASN cc_start: 0.9282 (m110) cc_final: 0.9075 (t0) REVERT: E 100 ARG cc_start: 0.9122 (ttp80) cc_final: 0.8714 (tpp-160) REVERT: E 128 GLU cc_start: 0.9391 (mp0) cc_final: 0.8994 (pp20) REVERT: E 132 ARG cc_start: 0.9338 (mtm110) cc_final: 0.8929 (mtm110) REVERT: E 141 ILE cc_start: 0.8865 (mt) cc_final: 0.8610 (mt) REVERT: E 144 MET cc_start: 0.8182 (ppp) cc_final: 0.7901 (ppp) REVERT: F 9 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8365 (pp30) REVERT: F 53 ASN cc_start: 0.8865 (t0) cc_final: 0.8579 (t0) REVERT: F 55 MET cc_start: 0.8798 (ttt) cc_final: 0.7470 (tmm) REVERT: F 70 LYS cc_start: 0.9576 (mmmm) cc_final: 0.9344 (mmmm) REVERT: F 79 GLU cc_start: 0.9616 (tt0) cc_final: 0.9299 (tp30) REVERT: F 81 ASP cc_start: 0.8909 (m-30) cc_final: 0.8682 (m-30) REVERT: F 103 ASP cc_start: 0.8956 (m-30) cc_final: 0.8722 (m-30) REVERT: F 132 ARG cc_start: 0.9696 (mtp-110) cc_final: 0.9493 (mtm110) REVERT: F 143 ARG cc_start: 0.9124 (mmm-85) cc_final: 0.8813 (mmm-85) REVERT: F 158 LYS cc_start: 0.8259 (mmpt) cc_final: 0.8034 (mmmt) REVERT: F 164 TYR cc_start: 0.7843 (t80) cc_final: 0.6796 (t80) REVERT: F 167 ARG cc_start: 0.8916 (ptt-90) cc_final: 0.8437 (ptt-90) REVERT: F 168 PHE cc_start: 0.9464 (t80) cc_final: 0.9194 (t80) REVERT: F 179 GLN cc_start: 0.9251 (tp-100) cc_final: 0.8981 (tp-100) REVERT: F 185 MET cc_start: 0.9150 (ptp) cc_final: 0.8923 (ptp) REVERT: F 190 LEU cc_start: 0.8909 (mt) cc_final: 0.8537 (mt) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.2734 time to fit residues: 156.4336 Evaluate side-chains 349 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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: 7.9990 chunk 122 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 34 optimal weight: 0.1980 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.089308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.063118 restraints weight = 62916.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066288 restraints weight = 35764.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.068595 restraints weight = 24400.865| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.7339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10566 Z= 0.265 Angle : 0.754 9.466 14366 Z= 0.394 Chirality : 0.048 0.188 1604 Planarity : 0.006 0.063 1882 Dihedral : 4.319 20.000 1404 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1310 helix: 0.66 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.45 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 23 HIS 0.003 0.001 HIS E 12 PHE 0.026 0.003 PHE B 168 TYR 0.015 0.002 TYR B 169 ARG 0.010 0.001 ARG E 173 ********************** 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 405 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.099 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: A 45 GLU cc_start: 0.9270 (tt0) cc_final: 0.8760 (pm20) REVERT: A 68 MET cc_start: 0.9381 (mtp) cc_final: 0.9013 (mtt) REVERT: A 98 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7556 (mt-10) REVERT: A 128 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8247 (tm-30) REVERT: A 129 ILE cc_start: 0.9170 (mt) cc_final: 0.8762 (mt) REVERT: A 143 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.8289 (ttm110) REVERT: A 163 ASP cc_start: 0.9038 (m-30) cc_final: 0.8815 (m-30) REVERT: A 167 ARG cc_start: 0.8864 (mtm-85) cc_final: 0.8387 (ptp90) REVERT: A 214 MET cc_start: 0.9158 (ptp) cc_final: 0.8933 (ptp) REVERT: A 215 MET cc_start: 0.8181 (ppp) cc_final: 0.7832 (ppp) REVERT: B 10 MET cc_start: 0.6394 (tmm) cc_final: 0.5886 (tmm) REVERT: B 29 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8913 (tm-30) REVERT: B 55 MET cc_start: 0.9605 (ttm) cc_final: 0.9268 (ttp) REVERT: B 72 THR cc_start: 0.9138 (p) cc_final: 0.8748 (p) REVERT: B 82 ARG cc_start: 0.8628 (tmm160) cc_final: 0.8409 (ptm-80) REVERT: B 100 ARG cc_start: 0.9054 (ttp80) cc_final: 0.8716 (tpm170) REVERT: B 128 GLU cc_start: 0.9474 (mp0) cc_final: 0.9121 (mp0) REVERT: B 129 ILE cc_start: 0.9523 (mm) cc_final: 0.9245 (tp) REVERT: B 141 ILE cc_start: 0.9463 (mt) cc_final: 0.9019 (mt) REVERT: B 167 ARG cc_start: 0.9339 (ttm110) cc_final: 0.9089 (ttm110) REVERT: C 68 MET cc_start: 0.9312 (mtp) cc_final: 0.8838 (mtt) REVERT: C 81 ASP cc_start: 0.9135 (m-30) cc_final: 0.8859 (m-30) REVERT: C 97 ARG cc_start: 0.8987 (ttp-110) cc_final: 0.8542 (ptt90) REVERT: C 103 ASP cc_start: 0.9089 (m-30) cc_final: 0.8859 (m-30) REVERT: C 129 ILE cc_start: 0.9663 (pt) cc_final: 0.9404 (pt) REVERT: C 134 ILE cc_start: 0.9545 (mm) cc_final: 0.9307 (mm) REVERT: C 154 ARG cc_start: 0.8485 (tpp80) cc_final: 0.8207 (mmm-85) REVERT: C 167 ARG cc_start: 0.9204 (ttt180) cc_final: 0.8754 (ptp90) REVERT: C 185 MET cc_start: 0.9086 (ptp) cc_final: 0.8708 (ptp) REVERT: C 215 MET cc_start: 0.8966 (ppp) cc_final: 0.8713 (ppp) REVERT: C 216 THR cc_start: 0.8449 (p) cc_final: 0.8246 (p) REVERT: D 68 MET cc_start: 0.8740 (mtt) cc_final: 0.8218 (mtt) REVERT: D 70 LYS cc_start: 0.9517 (mtpt) cc_final: 0.9195 (ptpt) REVERT: D 71 GLU cc_start: 0.8931 (pp20) cc_final: 0.8524 (pp20) REVERT: D 98 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6529 (tt0) REVERT: D 111 LEU cc_start: 0.9565 (tp) cc_final: 0.9345 (tp) REVERT: D 117 TRP cc_start: 0.8187 (m-10) cc_final: 0.7285 (m-90) REVERT: D 126 VAL cc_start: 0.8346 (t) cc_final: 0.7861 (t) REVERT: D 129 ILE cc_start: 0.9095 (tt) cc_final: 0.8861 (pt) REVERT: D 185 MET cc_start: 0.9528 (ptp) cc_final: 0.9103 (mtt) REVERT: D 187 GLU cc_start: 0.9102 (pt0) cc_final: 0.8685 (pp20) REVERT: D 212 GLU cc_start: 0.9256 (pt0) cc_final: 0.8812 (pm20) REVERT: D 215 MET cc_start: 0.8906 (mtm) cc_final: 0.8182 (mtm) REVERT: E 10 MET cc_start: 0.6000 (tmm) cc_final: 0.5559 (tmm) REVERT: E 28 GLU cc_start: 0.8677 (tt0) cc_final: 0.8183 (pt0) REVERT: E 30 LYS cc_start: 0.8901 (tppt) cc_final: 0.8386 (tptp) REVERT: E 55 MET cc_start: 0.9626 (ttm) cc_final: 0.9219 (tpp) REVERT: E 66 MET cc_start: 0.9086 (mpp) cc_final: 0.8615 (mpp) REVERT: E 68 MET cc_start: 0.9045 (mtp) cc_final: 0.8606 (mtp) REVERT: E 71 GLU cc_start: 0.8770 (pp20) cc_final: 0.8532 (pp20) REVERT: E 72 THR cc_start: 0.9192 (p) cc_final: 0.8780 (p) REVERT: E 74 ASN cc_start: 0.9307 (m110) cc_final: 0.9071 (t0) REVERT: E 100 ARG cc_start: 0.9165 (ttp80) cc_final: 0.8722 (tpp-160) REVERT: E 128 GLU cc_start: 0.9395 (mp0) cc_final: 0.8873 (tm-30) REVERT: E 129 ILE cc_start: 0.9473 (mm) cc_final: 0.8776 (mm) REVERT: E 131 LYS cc_start: 0.9764 (tptt) cc_final: 0.9542 (mmtt) REVERT: E 132 ARG cc_start: 0.9348 (mtm110) cc_final: 0.9029 (mtm110) REVERT: E 141 ILE cc_start: 0.8943 (mt) cc_final: 0.8685 (mt) REVERT: E 144 MET cc_start: 0.8149 (ppp) cc_final: 0.7858 (ppp) REVERT: F 9 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8318 (pp30) REVERT: F 10 MET cc_start: 0.8203 (ppp) cc_final: 0.7572 (tmm) REVERT: F 53 ASN cc_start: 0.8929 (t0) cc_final: 0.8646 (t0) REVERT: F 70 LYS cc_start: 0.9552 (mmmm) cc_final: 0.9343 (mmmm) REVERT: F 79 GLU cc_start: 0.9629 (tt0) cc_final: 0.9293 (tp30) REVERT: F 81 ASP cc_start: 0.8959 (m-30) cc_final: 0.8721 (m-30) REVERT: F 103 ASP cc_start: 0.8997 (m-30) cc_final: 0.8730 (m-30) REVERT: F 129 ILE cc_start: 0.9600 (pt) cc_final: 0.9357 (pt) REVERT: F 132 ARG cc_start: 0.9661 (mtp-110) cc_final: 0.9194 (mtp180) REVERT: F 143 ARG cc_start: 0.8975 (mmm-85) cc_final: 0.8593 (mmm-85) REVERT: F 164 TYR cc_start: 0.7968 (t80) cc_final: 0.6805 (t80) REVERT: F 167 ARG cc_start: 0.8930 (ptt-90) cc_final: 0.8455 (ptt-90) REVERT: F 168 PHE cc_start: 0.9526 (t80) cc_final: 0.9235 (t80) REVERT: F 179 GLN cc_start: 0.9230 (tp-100) cc_final: 0.8977 (tp-100) REVERT: F 185 MET cc_start: 0.9239 (ptp) cc_final: 0.8975 (ptp) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.2780 time to fit residues: 147.2766 Evaluate side-chains 333 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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: 0.8980 chunk 124 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 20 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.090567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.065168 restraints weight = 55473.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.068206 restraints weight = 32636.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.070406 restraints weight = 22670.340| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.7421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10566 Z= 0.223 Angle : 0.747 12.239 14366 Z= 0.382 Chirality : 0.047 0.162 1604 Planarity : 0.005 0.046 1882 Dihedral : 4.268 19.699 1404 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1310 helix: 0.61 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -0.36 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 23 HIS 0.002 0.000 HIS D 62 PHE 0.021 0.002 PHE B 168 TYR 0.013 0.002 TYR B 145 ARG 0.009 0.001 ARG D 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4074.33 seconds wall clock time: 73 minutes 42.15 seconds (4422.15 seconds total)