Starting phenix.real_space_refine on Mon Jul 28 05:38:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6slu_10240/07_2025/6slu_10240.cif Found real_map, /net/cci-nas-00/data/ceres_data/6slu_10240/07_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_10240/07_2025/6slu_10240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6slu_10240/07_2025/6slu_10240.map" model { file = "/net/cci-nas-00/data/ceres_data/6slu_10240/07_2025/6slu_10240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6slu_10240/07_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "C" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "D" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "F" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Time building chain proxies: 11.66, per 1000 atoms: 1.13 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: 4.28 Conformation dependent library (CDL) restraints added in 3.2 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: 1.52 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: 5.41 Time building geometry restraints manager: 3.71 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 37.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 37.850 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.240 ------------------------------------------------------------------------------- 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 : 0.006 0.505 10572 Z= 0.358 Angle : 0.753 44.137 14378 Z= 0.462 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 Details of bonding type rmsd hydrogen bonds : bond 0.13364 ( 577) hydrogen bonds : angle 4.66297 ( 1731) SS BOND : bond 0.21557 ( 6) SS BOND : angle 13.84675 ( 12) covalent geometry : bond 0.00352 (10566) covalent geometry : angle 0.63868 (14366) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 639 time to evaluate : 1.467 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: 0.2875 time to fit residues: 236.9283 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 : 1.145 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.098601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.070277 restraints weight = 71998.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.074198 restraints weight = 38425.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.077079 restraints weight = 25339.689| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 10572 Z= 0.142 Angle : 0.636 7.546 14378 Z= 0.321 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 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 577) hydrogen bonds : angle 3.79498 ( 1731) SS BOND : bond 0.00316 ( 6) SS BOND : angle 2.00455 ( 12) covalent geometry : bond 0.00320 (10566) covalent geometry : angle 0.63360 (14366) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 507 time to evaluate : 1.297 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: 0.5405 (tpt) cc_final: 0.4997 (mmm) REVERT: A 28 GLU cc_start: 0.8698 (tt0) cc_final: 0.8384 (pp20) REVERT: A 50 GLN cc_start: 0.9256 (tt0) cc_final: 0.8831 (tm-30) REVERT: A 51 ASP cc_start: 0.9298 (m-30) cc_final: 0.8849 (m-30) REVERT: A 68 MET cc_start: 0.9420 (mtp) cc_final: 0.8830 (mtt) REVERT: A 82 ARG cc_start: 0.9357 (ptm-80) cc_final: 0.9145 (ttp80) REVERT: A 129 ILE cc_start: 0.8855 (mt) cc_final: 0.8626 (tt) REVERT: A 141 ILE cc_start: 0.9622 (mm) cc_final: 0.9356 (tp) REVERT: A 144 MET cc_start: 0.9140 (tpp) cc_final: 0.8545 (tpp) REVERT: A 167 ARG cc_start: 0.9356 (mtm-85) cc_final: 0.8928 (ptt-90) REVERT: A 215 MET cc_start: 0.8524 (ptm) cc_final: 0.7890 (ptm) REVERT: B 10 MET cc_start: 0.5999 (tmm) cc_final: 0.5623 (tmm) REVERT: B 38 PRO cc_start: 0.9421 (Cg_exo) cc_final: 0.9207 (Cg_endo) REVERT: B 55 MET cc_start: 0.9545 (ttm) cc_final: 0.9101 (tpp) REVERT: B 96 MET cc_start: 0.4014 (mtm) cc_final: 0.3808 (mtt) REVERT: B 100 ARG cc_start: 0.8835 (ttp80) cc_final: 0.8609 (tpm170) REVERT: B 128 GLU cc_start: 0.9452 (mp0) cc_final: 0.8895 (pp20) REVERT: B 129 ILE cc_start: 0.9646 (mm) cc_final: 0.9006 (tp) REVERT: B 190 LEU cc_start: 0.8787 (mt) cc_final: 0.8268 (mt) REVERT: C 9 GLN cc_start: 0.8628 (tm-30) cc_final: 0.7997 (pm20) REVERT: C 25 LYS cc_start: 0.8694 (pttt) cc_final: 0.8259 (ttpt) REVERT: C 26 VAL cc_start: 0.8826 (p) cc_final: 0.8197 (p) REVERT: C 35 GLU cc_start: 0.8929 (pt0) cc_final: 0.8282 (tm-30) REVERT: C 53 ASN cc_start: 0.8571 (m-40) cc_final: 0.8354 (t0) REVERT: C 68 MET cc_start: 0.9455 (mtp) cc_final: 0.8724 (mtt) REVERT: C 98 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8745 (tm-30) REVERT: C 140 LYS cc_start: 0.9350 (mtmm) cc_final: 0.9118 (ptpp) REVERT: C 159 GLU cc_start: 0.8761 (mp0) cc_final: 0.8472 (pt0) REVERT: C 167 ARG cc_start: 0.8916 (ttt180) cc_final: 0.8678 (ptp90) REVERT: C 186 THR cc_start: 0.9032 (p) cc_final: 0.8740 (p) REVERT: C 215 MET cc_start: 0.8996 (ptp) cc_final: 0.8765 (ppp) REVERT: C 216 THR cc_start: 0.8644 (p) cc_final: 0.8019 (p) REVERT: D 16 SER cc_start: 0.9264 (t) cc_final: 0.8889 (p) REVERT: D 23 TRP cc_start: 0.9613 (t-100) cc_final: 0.9337 (t-100) REVERT: D 37 ILE cc_start: 0.9529 (mt) cc_final: 0.9202 (mt) REVERT: D 50 GLN cc_start: 0.9344 (tt0) cc_final: 0.8878 (tm-30) REVERT: D 51 ASP cc_start: 0.8705 (m-30) cc_final: 0.8096 (m-30) REVERT: D 55 MET cc_start: 0.9365 (ttm) cc_final: 0.9003 (ttp) REVERT: D 58 THR cc_start: 0.9283 (p) cc_final: 0.9070 (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: 0.9119 (mt) cc_final: 0.8647 (tt) REVERT: D 132 ARG cc_start: 0.9469 (mtp-110) cc_final: 0.9100 (ttp-110) REVERT: D 215 MET cc_start: 0.8858 (mtm) cc_final: 0.8378 (mtm) REVERT: E 28 GLU cc_start: 0.8877 (tt0) cc_final: 0.8476 (pt0) REVERT: E 30 LYS cc_start: 0.8923 (tppt) cc_final: 0.8315 (tptp) REVERT: E 55 MET cc_start: 0.9687 (ttm) cc_final: 0.9319 (tpp) REVERT: E 68 MET cc_start: 0.8970 (mtp) cc_final: 0.8750 (mtp) REVERT: E 100 ARG cc_start: 0.9144 (ttp80) cc_final: 0.8722 (tpp-160) REVERT: E 128 GLU cc_start: 0.9270 (mp0) cc_final: 0.8779 (tm-30) REVERT: E 129 ILE cc_start: 0.9514 (mm) cc_final: 0.8778 (mm) REVERT: E 141 ILE cc_start: 0.8821 (mt) cc_final: 0.8409 (mt) REVERT: E 190 LEU cc_start: 0.8871 (mt) cc_final: 0.8635 (mt) REVERT: F 13 GLN cc_start: 0.9380 (tp40) cc_final: 0.9166 (tp-100) REVERT: F 38 PRO cc_start: 0.9494 (Cg_exo) cc_final: 0.9275 (Cg_endo) REVERT: F 39 MET cc_start: 0.9236 (tpp) cc_final: 0.9022 (tpp) REVERT: F 68 MET cc_start: 0.9635 (mtp) cc_final: 0.8869 (mtt) REVERT: F 71 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8965 (tm-30) REVERT: F 75 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8525 (tm-30) REVERT: F 79 GLU cc_start: 0.9589 (tt0) cc_final: 0.9189 (tp30) REVERT: F 111 LEU cc_start: 0.9083 (tp) cc_final: 0.8260 (mp) REVERT: F 114 GLN cc_start: 0.8999 (mp-120) cc_final: 0.8133 (mp10) REVERT: F 117 TRP cc_start: 0.8319 (m-10) cc_final: 0.7523 (m-90) REVERT: F 129 ILE cc_start: 0.9660 (mt) cc_final: 0.9147 (mm) REVERT: F 132 ARG cc_start: 0.9451 (mtp-110) cc_final: 0.9095 (ptm-80) REVERT: F 158 LYS cc_start: 0.8494 (mmmt) cc_final: 0.8207 (mmmt) REVERT: F 164 TYR cc_start: 0.8139 (t80) cc_final: 0.7084 (t80) REVERT: F 185 MET cc_start: 0.8881 (ptp) cc_final: 0.8658 (ptp) REVERT: F 190 LEU cc_start: 0.8851 (mt) cc_final: 0.8395 (mt) outliers start: 1 outliers final: 0 residues processed: 508 average time/residue: 0.2863 time to fit residues: 188.1838 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 : 1.262 ------------------------------------------------------------------------------- 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: 2.9990 chunk 32 optimal weight: 0.0070 chunk 19 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 114 optimal weight: 0.0170 chunk 92 optimal weight: 2.9990 overall best weight: 1.3440 ------------------------------------------------------------------------------- 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 ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 95 GLN ** 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 = 0.3596 r_free = 0.3596 target = 0.097148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067524 restraints weight = 77097.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.071303 restraints weight = 41137.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.074073 restraints weight = 27267.541| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10572 Z= 0.141 Angle : 0.646 8.126 14378 Z= 0.327 Chirality : 0.045 0.159 1604 Planarity : 0.005 0.042 1882 Dihedral : 3.612 15.101 1404 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.18 % Allowed : 2.74 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1310 helix: 0.55 (0.18), residues: 818 sheet: None (None), residues: 0 loop : -0.69 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 23 HIS 0.004 0.000 HIS E 62 PHE 0.018 0.002 PHE B 40 TYR 0.009 0.001 TYR F 169 ARG 0.009 0.001 ARG E 167 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 577) hydrogen bonds : angle 3.84402 ( 1731) SS BOND : bond 0.00316 ( 6) SS BOND : angle 1.19126 ( 12) covalent geometry : bond 0.00303 (10566) covalent geometry : angle 0.64516 (14366) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 469 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.5562 (tpt) cc_final: 0.5343 (mmm) REVERT: A 45 GLU cc_start: 0.9120 (tt0) cc_final: 0.8646 (pm20) REVERT: A 68 MET cc_start: 0.9405 (mtp) cc_final: 0.9035 (mtt) REVERT: A 79 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8874 (tm-30) REVERT: A 98 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6807 (mt-10) REVERT: A 128 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 129 ILE cc_start: 0.9012 (mt) cc_final: 0.8589 (mt) REVERT: A 141 ILE cc_start: 0.9650 (mm) cc_final: 0.9360 (tp) REVERT: A 144 MET cc_start: 0.9118 (tpp) cc_final: 0.8517 (tpp) REVERT: A 167 ARG cc_start: 0.9341 (mtm-85) cc_final: 0.8883 (ptt-90) REVERT: A 187 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8907 (mt-10) REVERT: A 215 MET cc_start: 0.8422 (ptm) cc_final: 0.8009 (ptm) REVERT: B 10 MET cc_start: 0.6015 (tmm) cc_final: 0.5762 (tmm) REVERT: B 55 MET cc_start: 0.9585 (ttm) cc_final: 0.9056 (tpp) REVERT: B 68 MET cc_start: 0.9132 (mtt) cc_final: 0.8801 (mtt) REVERT: B 100 ARG cc_start: 0.8880 (ttp80) cc_final: 0.8621 (tpm170) REVERT: B 128 GLU cc_start: 0.9442 (mp0) cc_final: 0.8978 (pp20) REVERT: B 129 ILE cc_start: 0.9592 (mm) cc_final: 0.9354 (tp) REVERT: B 144 MET cc_start: 0.9044 (ppp) cc_final: 0.8736 (ppp) REVERT: B 190 LEU cc_start: 0.8858 (mt) cc_final: 0.8500 (mt) REVERT: C 9 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7839 (pm20) REVERT: C 66 MET cc_start: 0.9181 (mpp) cc_final: 0.8913 (mpp) REVERT: C 96 MET cc_start: 0.3150 (mpp) cc_final: 0.2268 (mpp) REVERT: C 159 GLU cc_start: 0.8771 (mp0) cc_final: 0.8464 (pt0) REVERT: C 167 ARG cc_start: 0.9034 (ttt180) cc_final: 0.8700 (ptp90) REVERT: D 16 SER cc_start: 0.9327 (t) cc_final: 0.8992 (p) REVERT: D 23 TRP cc_start: 0.9605 (t-100) cc_final: 0.9316 (t-100) REVERT: D 55 MET cc_start: 0.9372 (ttm) cc_final: 0.8977 (ttp) REVERT: D 68 MET cc_start: 0.9174 (mtt) cc_final: 0.8342 (mtt) REVERT: D 76 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7770 (mt-10) REVERT: D 104 ILE cc_start: 0.9204 (tt) cc_final: 0.8969 (tt) REVERT: D 132 ARG cc_start: 0.9421 (mtp-110) cc_final: 0.9122 (ttm110) REVERT: D 133 TRP cc_start: 0.8282 (m-10) cc_final: 0.8018 (m-10) REVERT: D 165 VAL cc_start: 0.9691 (p) cc_final: 0.9442 (m) REVERT: D 212 GLU cc_start: 0.9337 (pt0) cc_final: 0.8697 (pm20) REVERT: D 215 MET cc_start: 0.8731 (mtm) cc_final: 0.8088 (mtm) REVERT: E 13 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8559 (pp30) REVERT: E 28 GLU cc_start: 0.8809 (tt0) cc_final: 0.8316 (pt0) REVERT: E 30 LYS cc_start: 0.8845 (tppt) cc_final: 0.8229 (tptp) REVERT: E 32 PHE cc_start: 0.7051 (m-80) cc_final: 0.6800 (m-80) REVERT: E 55 MET cc_start: 0.9611 (ttm) cc_final: 0.9213 (tpp) REVERT: E 66 MET cc_start: 0.9011 (mpp) cc_final: 0.8639 (mpp) REVERT: E 68 MET cc_start: 0.9042 (mtp) cc_final: 0.8427 (mtp) REVERT: E 71 GLU cc_start: 0.8006 (pp20) cc_final: 0.7711 (pp20) REVERT: E 72 THR cc_start: 0.8768 (p) cc_final: 0.8211 (p) REVERT: E 100 ARG cc_start: 0.9116 (ttp80) cc_final: 0.8734 (tpp-160) REVERT: E 128 GLU cc_start: 0.9255 (mp0) cc_final: 0.8876 (tm-30) REVERT: E 129 ILE cc_start: 0.9481 (mm) cc_final: 0.8861 (mm) REVERT: E 131 LYS cc_start: 0.9665 (tttt) cc_final: 0.9436 (tptt) REVERT: E 132 ARG cc_start: 0.9336 (mtm110) cc_final: 0.9048 (mtm110) REVERT: E 141 ILE cc_start: 0.8539 (mt) cc_final: 0.8208 (mt) REVERT: E 144 MET cc_start: 0.7856 (ppp) cc_final: 0.7496 (ppp) REVERT: F 38 PRO cc_start: 0.9489 (Cg_exo) cc_final: 0.9269 (Cg_endo) REVERT: F 68 MET cc_start: 0.9214 (mtp) cc_final: 0.8881 (mtt) REVERT: F 75 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8437 (tm-30) REVERT: F 79 GLU cc_start: 0.9603 (tt0) cc_final: 0.9251 (tp30) REVERT: F 112 GLN cc_start: 0.9170 (mp10) cc_final: 0.8959 (mp10) REVERT: F 117 TRP cc_start: 0.7842 (m-10) cc_final: 0.7627 (m-90) REVERT: F 129 ILE cc_start: 0.9667 (mt) cc_final: 0.9216 (mm) REVERT: F 132 ARG cc_start: 0.9391 (mtp-110) cc_final: 0.9180 (ptm-80) REVERT: F 158 LYS cc_start: 0.8372 (mmmt) cc_final: 0.8096 (mmmt) REVERT: F 159 GLU cc_start: 0.7842 (pt0) cc_final: 0.7175 (pt0) REVERT: F 164 TYR cc_start: 0.8261 (t80) cc_final: 0.7092 (t80) REVERT: F 179 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8946 (tp-100) REVERT: F 185 MET cc_start: 0.8939 (ptp) cc_final: 0.8698 (ptp) REVERT: F 190 LEU cc_start: 0.9092 (mt) cc_final: 0.8775 (mt) outliers start: 2 outliers final: 0 residues processed: 471 average time/residue: 0.2752 time to fit residues: 167.8029 Evaluate side-chains 366 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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: 9.9990 chunk 74 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 113 optimal weight: 0.0010 chunk 108 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 4.7994 ------------------------------------------------------------------------------- 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** D 95 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN F 114 GLN F 155 GLN F 183 ASN ** 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 = 0.3499 r_free = 0.3499 target = 0.091113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.064304 restraints weight = 66431.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067589 restraints weight = 37285.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.069952 restraints weight = 25310.712| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10572 Z= 0.190 Angle : 0.696 8.108 14378 Z= 0.366 Chirality : 0.045 0.161 1604 Planarity : 0.005 0.049 1882 Dihedral : 3.889 20.297 1404 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.09 % Allowed : 3.19 % Favored : 96.73 % 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: 0.13 (0.22), residues: 1310 helix: 0.53 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.57 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 23 HIS 0.004 0.001 HIS D 12 PHE 0.018 0.003 PHE A 40 TYR 0.020 0.002 TYR B 145 ARG 0.012 0.001 ARG F 173 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 577) hydrogen bonds : angle 4.01353 ( 1731) SS BOND : bond 0.00074 ( 6) SS BOND : angle 0.73275 ( 12) covalent geometry : bond 0.00411 (10566) covalent geometry : angle 0.69575 (14366) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 434 time to evaluate : 1.144 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: A 68 MET cc_start: 0.9466 (mtp) cc_final: 0.9080 (mtt) REVERT: A 76 GLU cc_start: 0.8975 (mp0) cc_final: 0.8692 (mt-10) REVERT: A 100 ARG cc_start: 0.8888 (ptm-80) cc_final: 0.8607 (ptm-80) REVERT: A 128 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8201 (tm-30) REVERT: A 129 ILE cc_start: 0.9196 (mt) cc_final: 0.8698 (mt) REVERT: A 141 ILE cc_start: 0.9684 (mm) cc_final: 0.9441 (tp) REVERT: A 144 MET cc_start: 0.9105 (tpp) cc_final: 0.8579 (tpp) REVERT: A 163 ASP cc_start: 0.9099 (m-30) cc_final: 0.8297 (m-30) REVERT: A 167 ARG cc_start: 0.9287 (mtm-85) cc_final: 0.8780 (ptt-90) REVERT: A 214 MET cc_start: 0.9203 (ptp) cc_final: 0.8953 (ptp) REVERT: A 215 MET cc_start: 0.8446 (ptm) cc_final: 0.8152 (ptm) REVERT: B 10 MET cc_start: 0.5995 (tmm) cc_final: 0.5718 (tmm) REVERT: B 66 MET cc_start: 0.8966 (mpp) cc_final: 0.8690 (mpp) REVERT: B 71 GLU cc_start: 0.8797 (pp20) cc_final: 0.8593 (pp20) REVERT: B 72 THR cc_start: 0.9050 (p) cc_final: 0.8585 (p) REVERT: B 100 ARG cc_start: 0.8919 (ttp80) cc_final: 0.8640 (tpm170) REVERT: B 128 GLU cc_start: 0.9459 (mp0) cc_final: 0.8916 (pp20) REVERT: B 129 ILE cc_start: 0.9615 (mm) cc_final: 0.9384 (tp) REVERT: B 131 LYS cc_start: 0.9683 (tptt) cc_final: 0.9402 (mmtt) REVERT: B 141 ILE cc_start: 0.9111 (mt) cc_final: 0.8887 (mt) REVERT: B 144 MET cc_start: 0.8897 (ppp) cc_final: 0.8499 (ppp) REVERT: B 190 LEU cc_start: 0.9072 (mt) cc_final: 0.8759 (mt) REVERT: C 21 ASN cc_start: 0.9275 (m110) cc_final: 0.9055 (m110) REVERT: C 43 LEU cc_start: 0.9468 (tp) cc_final: 0.9227 (mm) REVERT: C 53 ASN cc_start: 0.9022 (t0) cc_final: 0.8789 (t0) REVERT: C 68 MET cc_start: 0.9463 (mtp) cc_final: 0.8797 (mtt) REVERT: C 71 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8856 (tm-30) REVERT: C 81 ASP cc_start: 0.9057 (m-30) cc_final: 0.8850 (m-30) REVERT: C 159 GLU cc_start: 0.9011 (mp0) cc_final: 0.8805 (mp0) REVERT: C 167 ARG cc_start: 0.9134 (ttt180) cc_final: 0.8726 (ptp-170) REVERT: D 23 TRP cc_start: 0.9640 (t-100) cc_final: 0.9334 (t-100) REVERT: D 55 MET cc_start: 0.9446 (ttm) cc_final: 0.8912 (ttm) REVERT: D 96 MET cc_start: 0.7412 (tpt) cc_final: 0.7144 (tpp) REVERT: D 98 GLU cc_start: 0.6437 (mt-10) cc_final: 0.6094 (mt-10) REVERT: D 117 TRP cc_start: 0.8096 (m-10) cc_final: 0.7316 (m-90) REVERT: D 126 VAL cc_start: 0.8301 (t) cc_final: 0.7882 (p) REVERT: D 129 ILE cc_start: 0.9175 (tt) cc_final: 0.8666 (pt) REVERT: D 163 ASP cc_start: 0.9068 (m-30) cc_final: 0.8122 (m-30) REVERT: D 167 ARG cc_start: 0.8975 (ptp-110) cc_final: 0.8398 (ptp-170) REVERT: D 181 VAL cc_start: 0.7793 (p) cc_final: 0.7569 (p) REVERT: D 185 MET cc_start: 0.8544 (mtt) cc_final: 0.8301 (ptp) REVERT: D 212 GLU cc_start: 0.9367 (pt0) cc_final: 0.8896 (pm20) REVERT: D 215 MET cc_start: 0.8931 (mtm) cc_final: 0.8398 (mtp) REVERT: E 28 GLU cc_start: 0.8827 (tt0) cc_final: 0.8379 (pt0) REVERT: E 30 LYS cc_start: 0.8892 (tppt) cc_final: 0.8280 (tptp) REVERT: E 55 MET cc_start: 0.9619 (ttm) cc_final: 0.9169 (tpp) REVERT: E 66 MET cc_start: 0.8807 (mpp) cc_final: 0.8379 (mpp) REVERT: E 68 MET cc_start: 0.9149 (mtp) cc_final: 0.8574 (mtp) REVERT: E 100 ARG cc_start: 0.9110 (ttp80) cc_final: 0.8710 (tpp-160) REVERT: E 128 GLU cc_start: 0.9345 (mp0) cc_final: 0.8823 (tm-30) REVERT: E 129 ILE cc_start: 0.9446 (mm) cc_final: 0.8932 (mm) REVERT: E 136 LEU cc_start: 0.9801 (tt) cc_final: 0.9434 (pp) REVERT: E 140 LYS cc_start: 0.9492 (mtpt) cc_final: 0.8955 (mtmm) REVERT: E 141 ILE cc_start: 0.8771 (mt) cc_final: 0.8464 (mt) REVERT: E 144 MET cc_start: 0.7900 (ppp) cc_final: 0.7570 (ppp) REVERT: E 179 GLN cc_start: 0.9429 (pm20) cc_final: 0.9056 (pm20) REVERT: F 13 GLN cc_start: 0.9456 (tp-100) cc_final: 0.9220 (tp40) REVERT: F 25 LYS cc_start: 0.8927 (ptmm) cc_final: 0.8715 (ttpp) REVERT: F 38 PRO cc_start: 0.9486 (Cg_exo) cc_final: 0.9241 (Cg_endo) REVERT: F 50 GLN cc_start: 0.9103 (mp10) cc_final: 0.8760 (mp10) REVERT: F 68 MET cc_start: 0.9279 (mtp) cc_final: 0.8795 (mtt) REVERT: F 75 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8400 (tm-30) REVERT: F 79 GLU cc_start: 0.9598 (tt0) cc_final: 0.9267 (tp30) REVERT: F 103 ASP cc_start: 0.8972 (m-30) cc_final: 0.8768 (m-30) REVERT: F 111 LEU cc_start: 0.9362 (mp) cc_final: 0.9137 (mp) REVERT: F 114 GLN cc_start: 0.8817 (mp10) cc_final: 0.8596 (mp10) REVERT: F 129 ILE cc_start: 0.9687 (mt) cc_final: 0.9431 (mm) REVERT: F 132 ARG cc_start: 0.9551 (mtp-110) cc_final: 0.9132 (ptm-80) REVERT: F 143 ARG cc_start: 0.9173 (mmm-85) cc_final: 0.8841 (mmm-85) REVERT: F 164 TYR cc_start: 0.8032 (t80) cc_final: 0.6798 (t80) REVERT: F 167 ARG cc_start: 0.8893 (mtm180) cc_final: 0.8518 (ptt-90) REVERT: F 168 PHE cc_start: 0.9473 (t80) cc_final: 0.9017 (t80) REVERT: F 176 GLN cc_start: 0.8137 (pp30) cc_final: 0.7643 (pp30) REVERT: F 185 MET cc_start: 0.9155 (ptp) cc_final: 0.8843 (ptp) REVERT: F 190 LEU cc_start: 0.9043 (mt) cc_final: 0.8682 (mt) outliers start: 1 outliers final: 0 residues processed: 435 average time/residue: 0.2812 time to fit residues: 157.9979 Evaluate side-chains 366 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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: 0.9990 chunk 82 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 E 12 HIS E 95 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.064058 restraints weight = 68668.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.067356 restraints weight = 37686.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.069788 restraints weight = 25427.422| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 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 = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10572 Z= 0.155 Angle : 0.669 7.791 14378 Z= 0.342 Chirality : 0.045 0.149 1604 Planarity : 0.005 0.069 1882 Dihedral : 3.939 17.686 1404 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.09 % Allowed : 2.12 % Favored : 97.79 % 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: 0.33 (0.23), residues: 1310 helix: 0.63 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.36 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 23 HIS 0.004 0.001 HIS B 62 PHE 0.019 0.002 PHE E 168 TYR 0.012 0.002 TYR C 169 ARG 0.010 0.001 ARG E 167 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 577) hydrogen bonds : angle 3.97936 ( 1731) SS BOND : bond 0.00145 ( 6) SS BOND : angle 1.27021 ( 12) covalent geometry : bond 0.00347 (10566) covalent geometry : angle 0.66821 (14366) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 430 time to evaluate : 1.378 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: A 68 MET cc_start: 0.9439 (mtp) cc_final: 0.8990 (mtt) REVERT: A 128 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 129 ILE cc_start: 0.9224 (mt) cc_final: 0.8811 (mt) REVERT: A 141 ILE cc_start: 0.9683 (mm) cc_final: 0.9434 (tp) REVERT: A 143 ARG cc_start: 0.8547 (mtt180) cc_final: 0.8295 (ttp-170) REVERT: A 144 MET cc_start: 0.9186 (tpp) cc_final: 0.8720 (tpp) REVERT: A 163 ASP cc_start: 0.9085 (m-30) cc_final: 0.8300 (m-30) REVERT: A 167 ARG cc_start: 0.9118 (mtm-85) cc_final: 0.8465 (ptt-90) REVERT: A 176 GLN cc_start: 0.8777 (pm20) cc_final: 0.8563 (pp30) REVERT: A 210 THR cc_start: 0.9258 (t) cc_final: 0.9052 (t) REVERT: A 214 MET cc_start: 0.9233 (ptp) cc_final: 0.8969 (ptp) REVERT: A 215 MET cc_start: 0.8544 (ptm) cc_final: 0.8188 (ptm) REVERT: B 10 MET cc_start: 0.6091 (tmm) cc_final: 0.5756 (tmm) REVERT: B 66 MET cc_start: 0.9037 (mpp) cc_final: 0.8765 (mpp) REVERT: B 100 ARG cc_start: 0.8928 (ttp80) cc_final: 0.8487 (tpm170) REVERT: B 128 GLU cc_start: 0.9429 (mp0) cc_final: 0.8876 (pp20) REVERT: B 129 ILE cc_start: 0.9597 (mm) cc_final: 0.9134 (tp) REVERT: B 144 MET cc_start: 0.8812 (ppp) cc_final: 0.8416 (ppp) REVERT: B 190 LEU cc_start: 0.9403 (mt) cc_final: 0.9005 (mt) REVERT: C 32 PHE cc_start: 0.8371 (m-80) cc_final: 0.8082 (m-80) REVERT: C 43 LEU cc_start: 0.9443 (tp) cc_final: 0.9230 (mm) REVERT: C 71 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8879 (tm-30) REVERT: C 81 ASP cc_start: 0.9014 (m-30) cc_final: 0.8806 (m-30) REVERT: C 117 TRP cc_start: 0.8262 (m-10) cc_final: 0.7419 (m-90) REVERT: C 167 ARG cc_start: 0.9160 (ttt180) cc_final: 0.8721 (ptp-170) REVERT: C 185 MET cc_start: 0.9104 (ptp) cc_final: 0.8670 (ptp) REVERT: D 23 TRP cc_start: 0.9641 (t-100) cc_final: 0.9296 (t-100) REVERT: D 55 MET cc_start: 0.9479 (ttm) cc_final: 0.8906 (ttm) REVERT: D 70 LYS cc_start: 0.9497 (mtpt) cc_final: 0.9223 (ptpt) REVERT: D 96 MET cc_start: 0.7433 (tpt) cc_final: 0.7230 (tpp) REVERT: D 98 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6276 (mt-10) REVERT: D 117 TRP cc_start: 0.8071 (m-10) cc_final: 0.7335 (m-90) REVERT: D 126 VAL cc_start: 0.8289 (t) cc_final: 0.7749 (t) REVERT: D 129 ILE cc_start: 0.8996 (tt) cc_final: 0.8562 (pt) REVERT: D 173 ARG cc_start: 0.9451 (ttm-80) cc_final: 0.9224 (ttp80) REVERT: D 212 GLU cc_start: 0.9339 (pt0) cc_final: 0.8856 (pm20) REVERT: D 214 MET cc_start: 0.9370 (mtm) cc_final: 0.9162 (mtt) REVERT: E 25 LYS cc_start: 0.9450 (tttp) cc_final: 0.9109 (ttmm) REVERT: E 28 GLU cc_start: 0.8827 (tt0) cc_final: 0.8248 (pt0) REVERT: E 30 LYS cc_start: 0.8907 (tppt) cc_final: 0.8278 (tptp) REVERT: E 55 MET cc_start: 0.9646 (ttm) cc_final: 0.9325 (tpp) REVERT: E 66 MET cc_start: 0.8956 (mpp) cc_final: 0.8588 (mpp) REVERT: E 68 MET cc_start: 0.9144 (mtp) cc_final: 0.8586 (mtp) REVERT: E 72 THR cc_start: 0.9010 (p) cc_final: 0.8447 (p) REVERT: E 100 ARG cc_start: 0.9098 (ttp80) cc_final: 0.8691 (tpp-160) REVERT: E 128 GLU cc_start: 0.9384 (mp0) cc_final: 0.9109 (mp0) REVERT: E 141 ILE cc_start: 0.8833 (mt) cc_final: 0.8569 (mt) REVERT: E 144 MET cc_start: 0.7974 (ppp) cc_final: 0.7646 (ppp) REVERT: F 13 GLN cc_start: 0.9466 (tp-100) cc_final: 0.9171 (tp-100) REVERT: F 38 PRO cc_start: 0.9457 (Cg_exo) cc_final: 0.9256 (Cg_endo) REVERT: F 70 LYS cc_start: 0.9543 (mmmm) cc_final: 0.9338 (mmmm) REVERT: F 75 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8373 (tm-30) REVERT: F 79 GLU cc_start: 0.9606 (tt0) cc_final: 0.9260 (tp30) REVERT: F 97 ARG cc_start: 0.9076 (ptp90) cc_final: 0.8728 (ttp-110) REVERT: F 117 TRP cc_start: 0.8091 (m-10) cc_final: 0.6955 (m-90) REVERT: F 143 ARG cc_start: 0.9014 (mmm-85) cc_final: 0.8811 (mmm-85) REVERT: F 158 LYS cc_start: 0.8332 (mmpt) cc_final: 0.8064 (tppt) REVERT: F 164 TYR cc_start: 0.7978 (t80) cc_final: 0.6756 (t80) REVERT: F 167 ARG cc_start: 0.8912 (mtm180) cc_final: 0.8689 (ptt-90) REVERT: F 168 PHE cc_start: 0.9500 (t80) cc_final: 0.8960 (t80) REVERT: F 179 GLN cc_start: 0.9329 (tp-100) cc_final: 0.9033 (tp-100) REVERT: F 182 LYS cc_start: 0.8451 (mtmt) cc_final: 0.8236 (ptpt) REVERT: F 185 MET cc_start: 0.9107 (ptp) cc_final: 0.8893 (ptp) REVERT: F 190 LEU cc_start: 0.9091 (mt) cc_final: 0.8720 (mt) REVERT: F 215 MET cc_start: 0.9273 (ppp) cc_final: 0.9056 (ppp) outliers start: 1 outliers final: 0 residues processed: 431 average time/residue: 0.2952 time to fit residues: 165.1223 Evaluate side-chains 363 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 13 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 22 optimal weight: 0.2980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3499 r_free = 0.3499 target = 0.090287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.063842 restraints weight = 76211.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.067268 restraints weight = 40565.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.069754 restraints weight = 26806.672| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.6393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10572 Z= 0.147 Angle : 0.674 8.221 14378 Z= 0.343 Chirality : 0.044 0.148 1604 Planarity : 0.005 0.044 1882 Dihedral : 4.019 18.486 1404 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 0.72 (0.18), residues: 838 sheet: None (None), residues: 0 loop : -0.42 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 23 HIS 0.003 0.001 HIS B 62 PHE 0.021 0.002 PHE A 40 TYR 0.012 0.002 TYR D 169 ARG 0.011 0.001 ARG E 167 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 577) hydrogen bonds : angle 3.96387 ( 1731) SS BOND : bond 0.00198 ( 6) SS BOND : angle 1.31569 ( 12) covalent geometry : bond 0.00331 (10566) covalent geometry : angle 0.67284 (14366) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 1.328 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: 0.9232 (t80) cc_final: 0.8978 (t80) REVERT: A 68 MET cc_start: 0.9455 (mtp) cc_final: 0.8998 (mtt) REVERT: A 71 GLU cc_start: 0.9512 (tm-30) cc_final: 0.9306 (tm-30) REVERT: A 128 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 129 ILE cc_start: 0.9190 (mt) cc_final: 0.8776 (mt) REVERT: A 144 MET cc_start: 0.9072 (tpp) cc_final: 0.8576 (tpp) REVERT: A 163 ASP cc_start: 0.9074 (m-30) cc_final: 0.8317 (m-30) REVERT: A 167 ARG cc_start: 0.9057 (mtm-85) cc_final: 0.8435 (ptt-90) REVERT: A 214 MET cc_start: 0.9226 (ptp) cc_final: 0.8990 (ptp) REVERT: A 215 MET cc_start: 0.8555 (ptm) cc_final: 0.8255 (ptm) REVERT: B 10 MET cc_start: 0.6433 (tmm) cc_final: 0.6083 (tmm) REVERT: B 100 ARG cc_start: 0.8922 (ttp80) cc_final: 0.8602 (tpm170) REVERT: B 128 GLU cc_start: 0.9442 (mp0) cc_final: 0.8965 (mp0) REVERT: B 129 ILE cc_start: 0.9557 (mm) cc_final: 0.9266 (mm) REVERT: B 132 ARG cc_start: 0.9659 (ptp-110) cc_final: 0.9402 (ptp-110) REVERT: B 141 ILE cc_start: 0.9129 (mt) cc_final: 0.8835 (mt) REVERT: B 144 MET cc_start: 0.8722 (ppp) cc_final: 0.8333 (ppp) REVERT: C 68 MET cc_start: 0.9490 (mtp) cc_final: 0.8982 (mtm) REVERT: C 71 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8848 (tm-30) REVERT: C 81 ASP cc_start: 0.8971 (m-30) cc_final: 0.8764 (m-30) REVERT: C 167 ARG cc_start: 0.9155 (ttt180) cc_final: 0.8690 (ptp-170) REVERT: C 185 MET cc_start: 0.9046 (ptp) cc_final: 0.8642 (ptp) REVERT: C 215 MET cc_start: 0.9016 (ppp) cc_final: 0.8801 (ppp) REVERT: D 55 MET cc_start: 0.9402 (ttm) cc_final: 0.9021 (ttm) REVERT: D 70 LYS cc_start: 0.9509 (mtpt) cc_final: 0.9278 (ptpt) REVERT: D 98 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6300 (mt-10) REVERT: D 117 TRP cc_start: 0.8068 (m-10) cc_final: 0.7143 (m-90) REVERT: D 126 VAL cc_start: 0.8298 (t) cc_final: 0.7791 (t) REVERT: D 129 ILE cc_start: 0.9105 (tt) cc_final: 0.8762 (pt) REVERT: D 132 ARG cc_start: 0.9541 (mtp-110) cc_final: 0.9047 (ttm110) REVERT: D 144 MET cc_start: 0.8657 (tmm) cc_final: 0.8283 (tmm) REVERT: D 159 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7127 (tm-30) REVERT: D 167 ARG cc_start: 0.9035 (ptp-110) cc_final: 0.8688 (ptp-170) REVERT: D 181 VAL cc_start: 0.7884 (p) cc_final: 0.7194 (p) REVERT: D 185 MET cc_start: 0.9547 (ptp) cc_final: 0.9181 (mtt) REVERT: D 212 GLU cc_start: 0.9344 (pt0) cc_final: 0.8987 (pm20) REVERT: D 214 MET cc_start: 0.9342 (mtm) cc_final: 0.9118 (mtt) REVERT: E 25 LYS cc_start: 0.9439 (tttp) cc_final: 0.9210 (ttmm) REVERT: E 28 GLU cc_start: 0.8775 (tt0) cc_final: 0.8292 (pt0) REVERT: E 30 LYS cc_start: 0.8899 (tppt) cc_final: 0.8366 (tptp) REVERT: E 55 MET cc_start: 0.9680 (ttm) cc_final: 0.9211 (tpp) REVERT: E 66 MET cc_start: 0.8930 (mpp) cc_final: 0.8512 (mpp) REVERT: E 68 MET cc_start: 0.9111 (mtp) cc_final: 0.8590 (mtp) REVERT: E 100 ARG cc_start: 0.9105 (ttp80) cc_final: 0.8686 (tpp-160) REVERT: E 128 GLU cc_start: 0.9397 (mp0) cc_final: 0.9095 (mp0) REVERT: E 141 ILE cc_start: 0.8829 (mt) cc_final: 0.8547 (mt) REVERT: E 144 MET cc_start: 0.8013 (ppp) cc_final: 0.7676 (ppp) REVERT: F 13 GLN cc_start: 0.9452 (tp-100) cc_final: 0.9175 (tp-100) REVERT: F 50 GLN cc_start: 0.9000 (mp10) cc_final: 0.8466 (mp10) REVERT: F 71 GLU cc_start: 0.8817 (pp20) cc_final: 0.8404 (pp20) REVERT: F 79 GLU cc_start: 0.9610 (tt0) cc_final: 0.9254 (tp30) REVERT: F 81 ASP cc_start: 0.9024 (m-30) cc_final: 0.8787 (m-30) REVERT: F 111 LEU cc_start: 0.9364 (mp) cc_final: 0.9158 (mp) REVERT: F 132 ARG cc_start: 0.9649 (mtp-110) cc_final: 0.9298 (ptm-80) REVERT: F 143 ARG cc_start: 0.8930 (mmm-85) cc_final: 0.8677 (mmm-85) REVERT: F 158 LYS cc_start: 0.8270 (mmpt) cc_final: 0.8058 (tppt) REVERT: F 164 TYR cc_start: 0.8006 (t80) cc_final: 0.6529 (t80) REVERT: F 167 ARG cc_start: 0.9133 (mtm180) cc_final: 0.8662 (ptt-90) REVERT: F 168 PHE cc_start: 0.9524 (t80) cc_final: 0.9059 (t80) REVERT: F 179 GLN cc_start: 0.9305 (tp-100) cc_final: 0.9049 (tp-100) REVERT: F 182 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8236 (ptpt) REVERT: F 185 MET cc_start: 0.9109 (ptp) cc_final: 0.8897 (ptp) REVERT: F 190 LEU cc_start: 0.9047 (mt) cc_final: 0.8717 (mt) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.2875 time to fit residues: 157.5879 Evaluate side-chains 348 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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: 3.9990 chunk 91 optimal weight: 0.0970 chunk 55 optimal weight: 0.3980 chunk 40 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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** E 95 GLN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 139 ASN ** 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 = 0.3517 r_free = 0.3517 target = 0.091619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.064067 restraints weight = 72219.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.067534 restraints weight = 39358.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.070078 restraints weight = 26300.689| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- 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 = 0.45 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10572 Z= 0.131 Angle : 0.674 8.542 14378 Z= 0.340 Chirality : 0.045 0.195 1604 Planarity : 0.005 0.047 1882 Dihedral : 4.087 17.936 1404 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 0.71 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -0.40 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 23 HIS 0.002 0.001 HIS C 12 PHE 0.020 0.002 PHE A 40 TYR 0.012 0.001 TYR C 164 ARG 0.012 0.001 ARG E 167 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 577) hydrogen bonds : angle 4.02271 ( 1731) SS BOND : bond 0.00677 ( 6) SS BOND : angle 1.33322 ( 12) covalent geometry : bond 0.00304 (10566) covalent geometry : angle 0.67320 (14366) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 1.278 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: A 40 PHE cc_start: 0.9191 (t80) cc_final: 0.8979 (t80) REVERT: A 68 MET cc_start: 0.9383 (mtp) cc_final: 0.9058 (mtt) REVERT: A 71 GLU cc_start: 0.9487 (tm-30) cc_final: 0.9215 (tm-30) REVERT: A 128 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8103 (tm-30) REVERT: A 129 ILE cc_start: 0.9188 (mt) cc_final: 0.8755 (mt) REVERT: A 144 MET cc_start: 0.9210 (tpp) cc_final: 0.8670 (tpp) REVERT: A 163 ASP cc_start: 0.9076 (m-30) cc_final: 0.8333 (m-30) REVERT: A 167 ARG cc_start: 0.9058 (mtm-85) cc_final: 0.8489 (ptt-90) REVERT: A 214 MET cc_start: 0.9236 (ptp) cc_final: 0.8983 (ptp) REVERT: A 215 MET cc_start: 0.8502 (ptm) cc_final: 0.8198 (ptm) REVERT: B 10 MET cc_start: 0.6484 (tmm) cc_final: 0.6100 (tmm) REVERT: B 55 MET cc_start: 0.9640 (ttm) cc_final: 0.9310 (ttm) REVERT: B 82 ARG cc_start: 0.8548 (tmm160) cc_final: 0.8302 (ttp80) REVERT: B 100 ARG cc_start: 0.8946 (ttp80) cc_final: 0.8670 (tpp-160) REVERT: B 128 GLU cc_start: 0.9446 (mp0) cc_final: 0.9022 (mp0) REVERT: B 129 ILE cc_start: 0.9490 (mm) cc_final: 0.9153 (tp) REVERT: B 212 GLU cc_start: 0.9323 (pt0) cc_final: 0.8974 (pm20) REVERT: C 68 MET cc_start: 0.9422 (mtp) cc_final: 0.8933 (mtm) REVERT: C 71 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8893 (tm-30) REVERT: C 81 ASP cc_start: 0.8999 (m-30) cc_final: 0.8784 (m-30) REVERT: C 97 ARG cc_start: 0.8873 (ttp-110) cc_final: 0.8442 (ptt-90) REVERT: C 117 TRP cc_start: 0.7995 (m-10) cc_final: 0.7246 (m-10) REVERT: C 129 ILE cc_start: 0.9649 (pt) cc_final: 0.9443 (pt) REVERT: C 143 ARG cc_start: 0.8622 (mtt180) cc_final: 0.8204 (mmt-90) REVERT: C 159 GLU cc_start: 0.8957 (mp0) cc_final: 0.8386 (pt0) REVERT: C 167 ARG cc_start: 0.9143 (ttt180) cc_final: 0.8691 (ptp90) REVERT: C 185 MET cc_start: 0.9052 (ptp) cc_final: 0.8658 (ptp) REVERT: C 215 MET cc_start: 0.9070 (ppp) cc_final: 0.8778 (ppp) REVERT: D 55 MET cc_start: 0.9492 (ttm) cc_final: 0.9240 (ttp) REVERT: D 70 LYS cc_start: 0.9493 (mtpt) cc_final: 0.9141 (ptpp) REVERT: D 98 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6520 (mt-10) REVERT: D 117 TRP cc_start: 0.8048 (m-10) cc_final: 0.7095 (m-90) REVERT: D 132 ARG cc_start: 0.9399 (mtp-110) cc_final: 0.8973 (ttm110) REVERT: D 173 ARG cc_start: 0.9398 (ttm-80) cc_final: 0.9116 (ttp80) REVERT: D 181 VAL cc_start: 0.7890 (p) cc_final: 0.7223 (p) REVERT: D 185 MET cc_start: 0.9408 (ptp) cc_final: 0.9164 (mtt) REVERT: D 212 GLU cc_start: 0.9317 (pt0) cc_final: 0.8989 (pm20) REVERT: E 25 LYS cc_start: 0.9447 (tttp) cc_final: 0.9113 (ttmm) REVERT: E 28 GLU cc_start: 0.8744 (tt0) cc_final: 0.8187 (pt0) REVERT: E 30 LYS cc_start: 0.8822 (tppt) cc_final: 0.8317 (tptp) REVERT: E 66 MET cc_start: 0.8908 (mpp) cc_final: 0.8439 (mpp) REVERT: E 68 MET cc_start: 0.9083 (mtp) cc_final: 0.8552 (mtp) REVERT: E 71 GLU cc_start: 0.8520 (pp20) cc_final: 0.8290 (pp20) REVERT: E 72 THR cc_start: 0.9011 (p) cc_final: 0.8496 (p) REVERT: E 74 ASN cc_start: 0.9260 (m110) cc_final: 0.9042 (t0) REVERT: E 100 ARG cc_start: 0.9111 (ttp80) cc_final: 0.8675 (tpp-160) REVERT: E 128 GLU cc_start: 0.9402 (mp0) cc_final: 0.9146 (mp0) REVERT: E 141 ILE cc_start: 0.8814 (mt) cc_final: 0.8527 (mt) REVERT: E 144 MET cc_start: 0.8084 (ppp) cc_final: 0.7734 (ppp) REVERT: E 215 MET cc_start: 0.8233 (tmm) cc_final: 0.8032 (tmm) REVERT: F 9 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8202 (pp30) REVERT: F 13 GLN cc_start: 0.9445 (tp-100) cc_final: 0.9173 (tp-100) REVERT: F 50 GLN cc_start: 0.8963 (mp10) cc_final: 0.8600 (mp10) REVERT: F 75 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8335 (tm-30) REVERT: F 79 GLU cc_start: 0.9617 (tt0) cc_final: 0.9280 (tp30) REVERT: F 81 ASP cc_start: 0.8968 (m-30) cc_final: 0.8651 (m-30) REVERT: F 103 ASP cc_start: 0.9023 (m-30) cc_final: 0.8573 (m-30) REVERT: F 143 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8615 (mmm-85) REVERT: F 158 LYS cc_start: 0.8300 (mmpt) cc_final: 0.8087 (tppt) REVERT: F 164 TYR cc_start: 0.7974 (t80) cc_final: 0.6787 (t80) REVERT: F 167 ARG cc_start: 0.9153 (mtm180) cc_final: 0.8681 (ptt-90) REVERT: F 168 PHE cc_start: 0.9501 (t80) cc_final: 0.9003 (t80) REVERT: F 179 GLN cc_start: 0.9323 (tp-100) cc_final: 0.9049 (tp-100) REVERT: F 182 LYS cc_start: 0.8417 (mtmt) cc_final: 0.8187 (ptpt) REVERT: F 190 LEU cc_start: 0.8921 (mt) cc_final: 0.8539 (mt) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.2955 time to fit residues: 162.8709 Evaluate side-chains 353 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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: 0.9980 chunk 9 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 34 optimal weight: 0.0270 chunk 41 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 overall best weight: 4.0044 ------------------------------------------------------------------------------- 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 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** F 50 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 = 0.3481 r_free = 0.3481 target = 0.089523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.062912 restraints weight = 66580.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.066166 restraints weight = 38060.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.068507 restraints weight = 25997.435| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.6978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10572 Z= 0.167 Angle : 0.710 9.003 14378 Z= 0.365 Chirality : 0.046 0.191 1604 Planarity : 0.005 0.042 1882 Dihedral : 4.169 20.184 1404 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: 0.43 (0.23), residues: 1310 helix: 0.78 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.47 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 23 HIS 0.006 0.001 HIS D 62 PHE 0.022 0.003 PHE B 168 TYR 0.015 0.002 TYR E 130 ARG 0.005 0.001 ARG D 82 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 577) hydrogen bonds : angle 4.18001 ( 1731) SS BOND : bond 0.00133 ( 6) SS BOND : angle 1.35611 ( 12) covalent geometry : bond 0.00380 (10566) covalent geometry : angle 0.70912 (14366) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.5720 (mmm) cc_final: 0.5358 (mmm) REVERT: A 55 MET cc_start: 0.9451 (ttm) cc_final: 0.9216 (ttp) REVERT: A 96 MET cc_start: 0.6210 (tpt) cc_final: 0.5749 (tpp) REVERT: A 98 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7303 (mt-10) REVERT: A 115 ILE cc_start: 0.9472 (mm) cc_final: 0.9261 (mm) REVERT: A 128 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 129 ILE cc_start: 0.9193 (mt) cc_final: 0.8790 (mt) REVERT: A 143 ARG cc_start: 0.8457 (mtt180) cc_final: 0.7937 (ttp-110) REVERT: A 144 MET cc_start: 0.9058 (tpp) cc_final: 0.8560 (tpp) REVERT: A 163 ASP cc_start: 0.9064 (m-30) cc_final: 0.8312 (m-30) REVERT: A 167 ARG cc_start: 0.9055 (mtm-85) cc_final: 0.8439 (ptt-90) REVERT: A 214 MET cc_start: 0.9308 (ptp) cc_final: 0.9020 (ptp) REVERT: A 215 MET cc_start: 0.8521 (ptm) cc_final: 0.8102 (ptm) REVERT: B 10 MET cc_start: 0.6331 (tmm) cc_final: 0.5825 (tmm) REVERT: B 32 PHE cc_start: 0.6483 (m-80) cc_final: 0.6271 (m-80) REVERT: B 55 MET cc_start: 0.9632 (ttm) cc_final: 0.9075 (ttp) REVERT: B 68 MET cc_start: 0.8921 (mtp) cc_final: 0.8494 (mtp) REVERT: B 72 THR cc_start: 0.9204 (p) cc_final: 0.8641 (p) REVERT: B 82 ARG cc_start: 0.8512 (tmm160) cc_final: 0.8108 (ttp80) REVERT: B 100 ARG cc_start: 0.8985 (ttp80) cc_final: 0.8695 (tpp-160) REVERT: B 128 GLU cc_start: 0.9436 (mp0) cc_final: 0.9070 (mp0) REVERT: B 141 ILE cc_start: 0.9200 (mt) cc_final: 0.8957 (mt) REVERT: B 144 MET cc_start: 0.8598 (ptm) cc_final: 0.8223 (mmt) REVERT: C 68 MET cc_start: 0.9429 (mtp) cc_final: 0.9047 (mtp) REVERT: C 71 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8880 (tm-30) REVERT: C 81 ASP cc_start: 0.9100 (m-30) cc_final: 0.8870 (m-30) REVERT: C 129 ILE cc_start: 0.9650 (pt) cc_final: 0.9389 (pt) REVERT: C 134 ILE cc_start: 0.9559 (mp) cc_final: 0.9302 (mp) REVERT: C 159 GLU cc_start: 0.9046 (mp0) cc_final: 0.8472 (pt0) REVERT: C 185 MET cc_start: 0.9048 (ptp) cc_final: 0.8694 (ptp) REVERT: C 215 MET cc_start: 0.9106 (ppp) cc_final: 0.8830 (ppp) REVERT: C 216 THR cc_start: 0.8373 (p) cc_final: 0.8080 (p) REVERT: D 70 LYS cc_start: 0.9496 (mtpt) cc_final: 0.9168 (ptpt) REVERT: D 98 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6651 (mt-10) REVERT: D 117 TRP cc_start: 0.8118 (m-10) cc_final: 0.7314 (m-90) REVERT: D 126 VAL cc_start: 0.8306 (t) cc_final: 0.7784 (t) REVERT: D 129 ILE cc_start: 0.9113 (tt) cc_final: 0.8789 (pt) REVERT: D 185 MET cc_start: 0.9424 (ptp) cc_final: 0.9161 (mtt) REVERT: D 212 GLU cc_start: 0.9435 (pt0) cc_final: 0.9012 (pm20) REVERT: E 25 LYS cc_start: 0.9431 (tttp) cc_final: 0.9204 (ttmm) REVERT: E 28 GLU cc_start: 0.8703 (tt0) cc_final: 0.8233 (pt0) REVERT: E 30 LYS cc_start: 0.8844 (tppt) cc_final: 0.8350 (tptp) REVERT: E 32 PHE cc_start: 0.6782 (m-80) cc_final: 0.6523 (m-80) REVERT: E 55 MET cc_start: 0.9624 (ttm) cc_final: 0.9188 (tpp) REVERT: E 66 MET cc_start: 0.8961 (mpp) cc_final: 0.8456 (mpp) REVERT: E 68 MET cc_start: 0.9160 (mtp) cc_final: 0.8616 (mtp) REVERT: E 71 GLU cc_start: 0.8603 (pp20) cc_final: 0.8400 (pp20) REVERT: E 72 THR cc_start: 0.8999 (p) cc_final: 0.8371 (p) REVERT: E 100 ARG cc_start: 0.9125 (ttp80) cc_final: 0.8674 (tpp-160) REVERT: E 128 GLU cc_start: 0.9429 (mp0) cc_final: 0.9148 (mp0) REVERT: E 141 ILE cc_start: 0.8904 (mt) cc_final: 0.8605 (mt) REVERT: E 144 MET cc_start: 0.8105 (ppp) cc_final: 0.7813 (ppp) REVERT: E 212 GLU cc_start: 0.9354 (pt0) cc_final: 0.9127 (pt0) REVERT: F 9 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8300 (pp30) REVERT: F 13 GLN cc_start: 0.9442 (tp-100) cc_final: 0.9160 (tp-100) REVERT: F 50 GLN cc_start: 0.8935 (mp10) cc_final: 0.8643 (mp10) REVERT: F 79 GLU cc_start: 0.9597 (tt0) cc_final: 0.9286 (tp30) REVERT: F 81 ASP cc_start: 0.9043 (m-30) cc_final: 0.8750 (m-30) REVERT: F 103 ASP cc_start: 0.9011 (m-30) cc_final: 0.8551 (m-30) REVERT: F 129 ILE cc_start: 0.9616 (pt) cc_final: 0.9200 (pt) REVERT: F 131 LYS cc_start: 0.9270 (pttm) cc_final: 0.8972 (pttm) REVERT: F 132 ARG cc_start: 0.9649 (mtp-110) cc_final: 0.9050 (ttp-110) REVERT: F 143 ARG cc_start: 0.8961 (mmm-85) cc_final: 0.8697 (mmm-85) REVERT: F 158 LYS cc_start: 0.8214 (mmpt) cc_final: 0.7953 (tppt) REVERT: F 164 TYR cc_start: 0.7956 (t80) cc_final: 0.6851 (t80) REVERT: F 167 ARG cc_start: 0.9122 (mtm180) cc_final: 0.8633 (ptt-90) REVERT: F 168 PHE cc_start: 0.9541 (t80) cc_final: 0.9057 (t80) REVERT: F 179 GLN cc_start: 0.9343 (tp-100) cc_final: 0.9047 (tp-100) REVERT: F 185 MET cc_start: 0.9128 (ptp) cc_final: 0.8881 (ptp) REVERT: F 190 LEU cc_start: 0.8810 (mt) cc_final: 0.8526 (mt) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.2700 time to fit residues: 142.7796 Evaluate side-chains 326 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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: 8.9990 chunk 3 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 113 optimal weight: 0.0050 chunk 108 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 overall best weight: 2.6098 ------------------------------------------------------------------------------- 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 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.090819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.062186 restraints weight = 90593.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.066006 restraints weight = 44809.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068784 restraints weight = 28519.732| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.7129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10572 Z= 0.144 Angle : 0.717 9.352 14378 Z= 0.365 Chirality : 0.047 0.186 1604 Planarity : 0.005 0.080 1882 Dihedral : 4.221 19.712 1404 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % 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: 0.41 (0.23), residues: 1310 helix: 0.77 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.48 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 23 HIS 0.003 0.001 HIS E 62 PHE 0.020 0.002 PHE B 168 TYR 0.013 0.002 TYR C 130 ARG 0.010 0.001 ARG E 173 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 577) hydrogen bonds : angle 4.18971 ( 1731) SS BOND : bond 0.00190 ( 6) SS BOND : angle 1.28940 ( 12) covalent geometry : bond 0.00336 (10566) covalent geometry : angle 0.71607 (14366) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 1.243 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: A 55 MET cc_start: 0.9439 (ttm) cc_final: 0.9192 (ttp) REVERT: A 98 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7400 (mt-10) REVERT: A 128 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 129 ILE cc_start: 0.9183 (mt) cc_final: 0.8765 (mt) REVERT: A 144 MET cc_start: 0.9108 (tpp) cc_final: 0.8508 (tpp) REVERT: A 163 ASP cc_start: 0.9077 (m-30) cc_final: 0.8279 (m-30) REVERT: A 167 ARG cc_start: 0.9078 (mtm-85) cc_final: 0.8497 (ptt-90) REVERT: A 214 MET cc_start: 0.9300 (ptp) cc_final: 0.9011 (ptp) REVERT: A 215 MET cc_start: 0.8595 (ptm) cc_final: 0.8193 (ptm) REVERT: B 10 MET cc_start: 0.6365 (tmm) cc_final: 0.5822 (tmm) REVERT: B 32 PHE cc_start: 0.6311 (m-80) cc_final: 0.5843 (m-80) REVERT: B 55 MET cc_start: 0.9638 (ttm) cc_final: 0.9294 (ttm) REVERT: B 72 THR cc_start: 0.9182 (p) cc_final: 0.8725 (p) REVERT: B 100 ARG cc_start: 0.9036 (ttp80) cc_final: 0.8709 (tpp-160) REVERT: B 128 GLU cc_start: 0.9429 (mp0) cc_final: 0.9087 (mp0) REVERT: B 141 ILE cc_start: 0.9230 (mt) cc_final: 0.8954 (mt) REVERT: B 212 GLU cc_start: 0.9343 (pt0) cc_final: 0.9112 (pt0) REVERT: C 32 PHE cc_start: 0.8478 (m-80) cc_final: 0.8191 (m-80) REVERT: C 68 MET cc_start: 0.9547 (mtp) cc_final: 0.8943 (mtt) REVERT: C 71 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8738 (tm-30) REVERT: C 81 ASP cc_start: 0.9022 (m-30) cc_final: 0.8816 (m-30) REVERT: C 129 ILE cc_start: 0.9619 (pt) cc_final: 0.9344 (pt) REVERT: C 134 ILE cc_start: 0.9585 (mp) cc_final: 0.9280 (mp) REVERT: C 138 LEU cc_start: 0.9741 (mt) cc_final: 0.9527 (mt) REVERT: C 167 ARG cc_start: 0.9219 (ttt180) cc_final: 0.8753 (ptp-170) REVERT: C 185 MET cc_start: 0.9072 (ptp) cc_final: 0.8710 (ptp) REVERT: C 215 MET cc_start: 0.9164 (ppp) cc_final: 0.8916 (ppp) REVERT: C 216 THR cc_start: 0.8407 (p) cc_final: 0.8088 (p) REVERT: D 40 PHE cc_start: 0.9378 (t80) cc_final: 0.9177 (t80) REVERT: D 68 MET cc_start: 0.8998 (mtt) cc_final: 0.8789 (mtt) REVERT: D 98 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6535 (tt0) REVERT: D 117 TRP cc_start: 0.8142 (m-10) cc_final: 0.7319 (m-90) REVERT: D 129 ILE cc_start: 0.9133 (tt) cc_final: 0.8810 (pt) REVERT: D 212 GLU cc_start: 0.9477 (pt0) cc_final: 0.9022 (pm20) REVERT: E 25 LYS cc_start: 0.9409 (tttp) cc_final: 0.9187 (ttmm) REVERT: E 28 GLU cc_start: 0.8681 (tt0) cc_final: 0.8199 (pt0) REVERT: E 30 LYS cc_start: 0.8899 (tppt) cc_final: 0.8391 (tptp) REVERT: E 55 MET cc_start: 0.9638 (ttm) cc_final: 0.9179 (tpp) REVERT: E 66 MET cc_start: 0.8978 (mpp) cc_final: 0.8565 (mpp) REVERT: E 68 MET cc_start: 0.9133 (mtp) cc_final: 0.8578 (mtp) REVERT: E 71 GLU cc_start: 0.8600 (pp20) cc_final: 0.8344 (pp20) REVERT: E 72 THR cc_start: 0.8956 (p) cc_final: 0.8606 (p) REVERT: E 74 ASN cc_start: 0.9271 (m110) cc_final: 0.8977 (t0) REVERT: E 100 ARG cc_start: 0.9133 (ttp80) cc_final: 0.8693 (tpp-160) REVERT: E 128 GLU cc_start: 0.9437 (mp0) cc_final: 0.9151 (mp0) REVERT: E 141 ILE cc_start: 0.8911 (mt) cc_final: 0.8670 (mt) REVERT: E 144 MET cc_start: 0.8153 (ppp) cc_final: 0.7871 (ppp) REVERT: F 9 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8314 (pp30) REVERT: F 13 GLN cc_start: 0.9361 (tp-100) cc_final: 0.9083 (tp-100) REVERT: F 39 MET cc_start: 0.9228 (tpp) cc_final: 0.8964 (tpp) REVERT: F 50 GLN cc_start: 0.8932 (mp10) cc_final: 0.8621 (mp10) REVERT: F 79 GLU cc_start: 0.9602 (tt0) cc_final: 0.9281 (tp30) REVERT: F 81 ASP cc_start: 0.8992 (m-30) cc_final: 0.8732 (m-30) REVERT: F 103 ASP cc_start: 0.9012 (m-30) cc_final: 0.8796 (m-30) REVERT: F 131 LYS cc_start: 0.9293 (pttm) cc_final: 0.9004 (pttm) REVERT: F 132 ARG cc_start: 0.9647 (mtp-110) cc_final: 0.9376 (mtp-110) REVERT: F 143 ARG cc_start: 0.8958 (mmm-85) cc_final: 0.8690 (mmm-85) REVERT: F 158 LYS cc_start: 0.8235 (mmpt) cc_final: 0.7997 (mmmt) REVERT: F 164 TYR cc_start: 0.7931 (t80) cc_final: 0.6593 (t80) REVERT: F 167 ARG cc_start: 0.9107 (mtm180) cc_final: 0.8567 (ptt-90) REVERT: F 168 PHE cc_start: 0.9535 (t80) cc_final: 0.9131 (t80) REVERT: F 179 GLN cc_start: 0.9218 (tp-100) cc_final: 0.8986 (tp-100) REVERT: F 185 MET cc_start: 0.9042 (ptp) cc_final: 0.8839 (ptp) REVERT: F 190 LEU cc_start: 0.8774 (mt) cc_final: 0.8484 (mt) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.3051 time to fit residues: 166.9146 Evaluate side-chains 342 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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: 9.9990 chunk 38 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 0.0010 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 overall best weight: 3.3392 ------------------------------------------------------------------------------- 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 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.088719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.063057 restraints weight = 61896.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.066204 restraints weight = 35969.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.068490 restraints weight = 24725.112| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.7330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10572 Z= 0.158 Angle : 0.740 9.739 14378 Z= 0.381 Chirality : 0.047 0.176 1604 Planarity : 0.005 0.042 1882 Dihedral : 4.301 19.329 1404 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: 0.28 (0.23), residues: 1310 helix: 0.68 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.54 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 23 HIS 0.005 0.001 HIS F 62 PHE 0.028 0.003 PHE E 32 TYR 0.014 0.002 TYR B 169 ARG 0.008 0.001 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 577) hydrogen bonds : angle 4.26809 ( 1731) SS BOND : bond 0.00136 ( 6) SS BOND : angle 1.27251 ( 12) covalent geometry : bond 0.00365 (10566) covalent geometry : angle 0.73955 (14366) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 1.157 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 28 GLU cc_start: 0.9193 (mm-30) cc_final: 0.7891 (pp20) REVERT: A 29 GLU cc_start: 0.7921 (pt0) cc_final: 0.7339 (pt0) REVERT: A 40 PHE cc_start: 0.9322 (t80) cc_final: 0.9005 (t80) REVERT: A 55 MET cc_start: 0.9496 (ttm) cc_final: 0.9244 (ttp) REVERT: A 98 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7427 (mt-10) REVERT: A 115 ILE cc_start: 0.9465 (mm) cc_final: 0.9206 (pt) REVERT: A 128 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8193 (tm-30) REVERT: A 129 ILE cc_start: 0.9153 (mt) cc_final: 0.8756 (mt) REVERT: A 163 ASP cc_start: 0.9035 (m-30) cc_final: 0.8283 (m-30) REVERT: A 167 ARG cc_start: 0.9098 (mtm-85) cc_final: 0.8539 (ptt-90) REVERT: A 214 MET cc_start: 0.9360 (ptp) cc_final: 0.9064 (ptp) REVERT: A 215 MET cc_start: 0.8607 (ptm) cc_final: 0.8153 (ptm) REVERT: B 10 MET cc_start: 0.6361 (tmm) cc_final: 0.6011 (tmm) REVERT: B 32 PHE cc_start: 0.6540 (m-80) cc_final: 0.6094 (m-80) REVERT: B 55 MET cc_start: 0.9616 (ttm) cc_final: 0.9287 (ttm) REVERT: B 72 THR cc_start: 0.9117 (p) cc_final: 0.8704 (p) REVERT: B 100 ARG cc_start: 0.9055 (ttp80) cc_final: 0.8707 (tpm170) REVERT: B 128 GLU cc_start: 0.9399 (mp0) cc_final: 0.9076 (mp0) REVERT: C 68 MET cc_start: 0.9496 (mtp) cc_final: 0.8873 (mtt) REVERT: C 71 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8863 (tm-30) REVERT: C 81 ASP cc_start: 0.9093 (m-30) cc_final: 0.8871 (m-30) REVERT: C 129 ILE cc_start: 0.9590 (pt) cc_final: 0.9282 (pt) REVERT: C 131 LYS cc_start: 0.9402 (ptpp) cc_final: 0.9161 (pttt) REVERT: C 134 ILE cc_start: 0.9585 (mp) cc_final: 0.9356 (mp) REVERT: C 138 LEU cc_start: 0.9728 (mt) cc_final: 0.9520 (mt) REVERT: C 154 ARG cc_start: 0.8387 (tpp80) cc_final: 0.8146 (mmm-85) REVERT: C 167 ARG cc_start: 0.9213 (ttt180) cc_final: 0.8769 (ptp-170) REVERT: C 185 MET cc_start: 0.9066 (ptp) cc_final: 0.8731 (ptp) REVERT: C 215 MET cc_start: 0.9186 (ppp) cc_final: 0.8836 (ppp) REVERT: C 216 THR cc_start: 0.8668 (p) cc_final: 0.8316 (p) REVERT: D 98 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6536 (mt-10) REVERT: D 117 TRP cc_start: 0.7946 (m-10) cc_final: 0.7190 (m-90) REVERT: D 211 LEU cc_start: 0.9731 (tp) cc_final: 0.9494 (tp) REVERT: D 212 GLU cc_start: 0.9376 (pt0) cc_final: 0.8952 (pm20) REVERT: D 214 MET cc_start: 0.9146 (ptp) cc_final: 0.8875 (ptp) REVERT: E 25 LYS cc_start: 0.9373 (tttp) cc_final: 0.9083 (ttmm) REVERT: E 28 GLU cc_start: 0.8769 (tt0) cc_final: 0.8211 (pt0) REVERT: E 30 LYS cc_start: 0.8903 (tppt) cc_final: 0.8402 (tptp) REVERT: E 32 PHE cc_start: 0.7191 (m-80) cc_final: 0.6828 (m-80) REVERT: E 55 MET cc_start: 0.9609 (ttm) cc_final: 0.9148 (tpp) REVERT: E 66 MET cc_start: 0.9227 (mpp) cc_final: 0.8589 (mpp) REVERT: E 68 MET cc_start: 0.9166 (mtp) cc_final: 0.8670 (mtp) REVERT: E 71 GLU cc_start: 0.8812 (pp20) cc_final: 0.8592 (pp20) REVERT: E 72 THR cc_start: 0.9174 (p) cc_final: 0.8655 (p) REVERT: E 100 ARG cc_start: 0.9160 (ttp80) cc_final: 0.8723 (tpp-160) REVERT: E 128 GLU cc_start: 0.9426 (mp0) cc_final: 0.9142 (mp0) REVERT: E 141 ILE cc_start: 0.9232 (mt) cc_final: 0.8585 (mt) REVERT: E 144 MET cc_start: 0.7672 (ppp) cc_final: 0.7404 (ppp) REVERT: F 9 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8352 (pp30) REVERT: F 13 GLN cc_start: 0.9337 (tp-100) cc_final: 0.9080 (tp40) REVERT: F 39 MET cc_start: 0.9249 (tpp) cc_final: 0.9018 (tpp) REVERT: F 50 GLN cc_start: 0.8904 (mp10) cc_final: 0.8657 (mp10) REVERT: F 68 MET cc_start: 0.9232 (mtp) cc_final: 0.8999 (mtp) REVERT: F 79 GLU cc_start: 0.9625 (tt0) cc_final: 0.9307 (tp30) REVERT: F 81 ASP cc_start: 0.9062 (m-30) cc_final: 0.8783 (m-30) REVERT: F 103 ASP cc_start: 0.9012 (m-30) cc_final: 0.8571 (m-30) REVERT: F 131 LYS cc_start: 0.9321 (pttm) cc_final: 0.9098 (pttm) REVERT: F 132 ARG cc_start: 0.9618 (mtp-110) cc_final: 0.9406 (mtp-110) REVERT: F 143 ARG cc_start: 0.9043 (mmm-85) cc_final: 0.8763 (mmm-85) REVERT: F 158 LYS cc_start: 0.8296 (mmpt) cc_final: 0.8085 (mmmt) REVERT: F 164 TYR cc_start: 0.8008 (t80) cc_final: 0.6620 (t80) REVERT: F 167 ARG cc_start: 0.9083 (mtm180) cc_final: 0.8563 (ptt-90) REVERT: F 168 PHE cc_start: 0.9516 (t80) cc_final: 0.9110 (t80) REVERT: F 185 MET cc_start: 0.9058 (ptp) cc_final: 0.8829 (ptp) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.2959 time to fit residues: 155.5823 Evaluate side-chains 342 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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: 2.9990 chunk 124 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 59 optimal weight: 0.0870 chunk 88 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 overall best weight: 2.9364 ------------------------------------------------------------------------------- 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 183 ASN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3470 r_free = 0.3470 target = 0.088761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.063722 restraints weight = 54867.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.066697 restraints weight = 33156.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.068844 restraints weight = 23319.062| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.7468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10572 Z= 0.152 Angle : 0.748 10.173 14378 Z= 0.382 Chirality : 0.047 0.171 1604 Planarity : 0.005 0.042 1882 Dihedral : 4.282 18.283 1404 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.29 (0.23), residues: 1310 helix: 0.65 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -0.47 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 23 HIS 0.003 0.001 HIS C 12 PHE 0.025 0.002 PHE E 32 TYR 0.014 0.002 TYR B 169 ARG 0.013 0.001 ARG B 82 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 577) hydrogen bonds : angle 4.30269 ( 1731) SS BOND : bond 0.00170 ( 6) SS BOND : angle 1.27164 ( 12) covalent geometry : bond 0.00355 (10566) covalent geometry : angle 0.74743 (14366) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4478.47 seconds wall clock time: 78 minutes 23.03 seconds (4703.03 seconds total)