Starting phenix.real_space_refine on Tue Mar 3 23:33:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ch6_30369/03_2026/7ch6_30369_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ch6_30369/03_2026/7ch6_30369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ch6_30369/03_2026/7ch6_30369_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ch6_30369/03_2026/7ch6_30369_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ch6_30369/03_2026/7ch6_30369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ch6_30369/03_2026/7ch6_30369.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 58 5.16 5 C 5934 2.51 5 N 1584 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9260 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1871 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "B" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1871 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2006 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 18, 'TRANS': 246} Chain: "D" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2006 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 18, 'TRANS': 246} Chain: "E" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.21, per 1000 atoms: 0.24 Number of scatterers: 9260 At special positions: 0 Unit cell: (105.04, 109.2, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 6 15.00 O 1678 8.00 N 1584 7.00 C 5934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.59 Conformation dependent library (CDL) restraints added in 379.2 milliseconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 57.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 13 through 29 removed outlier: 3.684A pdb=" N LEU A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THR A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.855A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.804A pdb=" N SER A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 86 through 96 removed outlier: 3.605A pdb=" N LEU A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.837A pdb=" N VAL A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 138 through 152 removed outlier: 4.935A pdb=" N SER A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 154 through 175 removed outlier: 3.842A pdb=" N VAL A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 195 through 217 removed outlier: 3.602A pdb=" N LEU A 199 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 259 removed outlier: 3.544A pdb=" N SER A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 29 removed outlier: 4.914A pdb=" N THR B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHE B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.855A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 79 removed outlier: 3.803A pdb=" N SER B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 86 through 96 removed outlier: 3.605A pdb=" N LEU B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 115 removed outlier: 3.838A pdb=" N VAL B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 138 through 152 removed outlier: 4.934A pdb=" N SER B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.841A pdb=" N VAL B 160 " --> pdb=" O PRO B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 195 through 217 removed outlier: 3.603A pdb=" N LEU B 199 " --> pdb=" O TRP B 195 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 205 " --> pdb=" O ASN B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 259 removed outlier: 3.544A pdb=" N SER B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 78 through 85 removed outlier: 3.992A pdb=" N THR C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 107 through 114 Processing helix chain 'C' and resid 117 through 133 removed outlier: 3.575A pdb=" N SER C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 159 removed outlier: 3.699A pdb=" N ALA C 150 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 194 removed outlier: 3.628A pdb=" N ILE C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN C 191 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 228 through 233 removed outlier: 3.903A pdb=" N GLN C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 246 removed outlier: 3.978A pdb=" N PHE C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 78 through 85 removed outlier: 3.991A pdb=" N THR D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 107 through 114 Processing helix chain 'D' and resid 117 through 133 removed outlier: 3.576A pdb=" N SER D 123 " --> pdb=" O PRO D 119 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 159 removed outlier: 3.699A pdb=" N ALA D 150 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.628A pdb=" N ILE D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 228 through 233 removed outlier: 3.902A pdb=" N GLN D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 246 removed outlier: 3.977A pdb=" N PHE D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 266 Processing helix chain 'E' and resid 25 through 31 removed outlier: 3.504A pdb=" N TRP E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET E 31 " --> pdb=" O PRO E 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 25 through 31' Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 51 through 68 removed outlier: 3.596A pdb=" N GLN E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 88 removed outlier: 3.658A pdb=" N TYR E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 31 removed outlier: 3.504A pdb=" N TRP F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET F 31 " --> pdb=" O PRO F 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 31' Processing helix chain 'F' and resid 31 through 36 Processing helix chain 'F' and resid 51 through 68 removed outlier: 3.598A pdb=" N GLN F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 88 removed outlier: 3.658A pdb=" N TYR F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 32 removed outlier: 5.797A pdb=" N ILE C 27 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 13 " --> pdb=" O ILE C 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 88 through 90 removed outlier: 7.144A pdb=" N ILE C 166 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL C 201 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE C 168 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C 37 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N SER C 202 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE C 39 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA C 38 " --> pdb=" O TRP C 216 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU C 218 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N MET C 40 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 27 through 32 removed outlier: 5.797A pdb=" N ILE D 27 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP D 13 " --> pdb=" O ILE D 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 88 through 90 removed outlier: 7.143A pdb=" N ILE D 166 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL D 201 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE D 168 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR D 37 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N SER D 202 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE D 39 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA D 38 " --> pdb=" O TRP D 216 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU D 218 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N MET D 40 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AA6, first strand: chain 'E' and resid 42 through 43 removed outlier: 6.786A pdb=" N ILE E 42 " --> pdb=" O GLN E 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 9 Processing sheet with id=AA8, first strand: chain 'F' and resid 42 through 43 removed outlier: 6.785A pdb=" N ILE F 42 " --> pdb=" O GLN F 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 422 hydrogen bonds defined for protein. 1254 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: 1.37 Time building geometry restraints manager: 0.82 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: 3003 1.34 - 1.46: 1620 1.46 - 1.57: 4695 1.57 - 1.69: 10 1.69 - 1.81: 108 Bond restraints: 9436 Sorted by residual: bond pdb=" N3B ANP C 301 " pdb=" PG ANP C 301 " ideal model delta sigma weight residual 1.795 1.630 0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" N3B ANP D 301 " pdb=" PG ANP D 301 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" O3A ANP C 301 " pdb=" PB ANP C 301 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O3A ANP D 301 " pdb=" PB ANP D 301 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O5' ANP D 301 " pdb=" PA ANP D 301 " ideal model delta sigma weight residual 1.655 1.602 0.053 2.00e-02 2.50e+03 7.07e+00 ... (remaining 9431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 12423 1.92 - 3.83: 329 3.83 - 5.75: 70 5.75 - 7.67: 6 7.67 - 9.59: 6 Bond angle restraints: 12834 Sorted by residual: angle pdb=" C ASP C 204 " pdb=" N VAL C 205 " pdb=" CA VAL C 205 " ideal model delta sigma weight residual 120.43 124.33 -3.90 9.60e-01 1.09e+00 1.65e+01 angle pdb=" C ASP D 204 " pdb=" N VAL D 205 " pdb=" CA VAL D 205 " ideal model delta sigma weight residual 120.43 124.33 -3.90 9.60e-01 1.09e+00 1.65e+01 angle pdb=" C VAL C 205 " pdb=" CA VAL C 205 " pdb=" CB VAL C 205 " ideal model delta sigma weight residual 113.70 110.36 3.34 9.50e-01 1.11e+00 1.24e+01 angle pdb=" C VAL D 205 " pdb=" CA VAL D 205 " pdb=" CB VAL D 205 " ideal model delta sigma weight residual 113.70 110.40 3.30 9.50e-01 1.11e+00 1.20e+01 angle pdb=" N3B ANP D 301 " pdb=" PG ANP D 301 " pdb=" O2G ANP D 301 " ideal model delta sigma weight residual 101.05 110.61 -9.56 3.00e+00 1.11e-01 1.02e+01 ... (remaining 12829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.78: 5261 23.78 - 47.56: 314 47.56 - 71.34: 78 71.34 - 95.12: 11 95.12 - 118.89: 4 Dihedral angle restraints: 5668 sinusoidal: 2228 harmonic: 3440 Sorted by residual: dihedral pdb=" CA LEU E 95 " pdb=" C LEU E 95 " pdb=" N PRO E 96 " pdb=" CA PRO E 96 " ideal model delta harmonic sigma weight residual -180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LEU F 95 " pdb=" C LEU F 95 " pdb=" N PRO F 96 " pdb=" CA PRO F 96 " ideal model delta harmonic sigma weight residual -180.00 -152.78 -27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA MET B 134 " pdb=" C MET B 134 " pdb=" N MET B 135 " pdb=" CA MET B 135 " ideal model delta harmonic sigma weight residual 180.00 156.33 23.67 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 5665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.951: 1535 0.951 - 1.902: 0 1.902 - 2.853: 0 2.853 - 3.803: 0 3.803 - 4.754: 1 Chirality restraints: 1536 Sorted by residual: chirality pdb=" C1' ANP C 301 " pdb=" C2' ANP C 301 " pdb=" N9 ANP C 301 " pdb=" O4' ANP C 301 " both_signs ideal model delta sigma weight residual False 2.42 -2.33 4.75 2.00e-01 2.50e+01 5.65e+02 chirality pdb=" C3' ANP C 301 " pdb=" C2' ANP C 301 " pdb=" C4' ANP C 301 " pdb=" O3' ANP C 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C3' ANP D 301 " pdb=" C2' ANP D 301 " pdb=" C4' ANP D 301 " pdb=" O3' ANP D 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1533 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 95 " -0.078 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO E 96 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 95 " 0.078 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO F 96 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO F 96 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO F 96 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 41 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO B 42 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 42 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 42 " 0.021 5.00e-02 4.00e+02 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 160 2.64 - 3.21: 9166 3.21 - 3.77: 14614 3.77 - 4.34: 20172 4.34 - 4.90: 33320 Nonbonded interactions: 77432 Sorted by model distance: nonbonded pdb=" N3 ANP C 301 " pdb=" O2' ANP C 301 " model vdw 2.077 3.120 nonbonded pdb=" OG SER B 130 " pdb=" OE1 GLN C 57 " model vdw 2.104 3.040 nonbonded pdb=" OG SER A 228 " pdb=" OG SER B 228 " model vdw 2.117 3.040 nonbonded pdb=" OG SER A 131 " pdb=" NH2 ARG D 157 " model vdw 2.117 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 62 " model vdw 2.128 3.040 ... (remaining 77427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.560 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.008 0.165 9436 Z= 0.355 Angle : 0.821 9.587 12834 Z= 0.451 Chirality : 0.130 4.754 1536 Planarity : 0.006 0.118 1606 Dihedral : 16.465 118.895 3456 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 12.88 % Allowed : 11.87 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.53 (0.20), residues: 1202 helix: -2.92 (0.15), residues: 650 sheet: -0.75 (0.94), residues: 40 loop : -3.21 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 97 TYR 0.011 0.002 TYR D 256 PHE 0.015 0.002 PHE A 162 TRP 0.011 0.001 TRP B 195 HIS 0.004 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00784 ( 9436) covalent geometry : angle 0.82134 (12834) hydrogen bonds : bond 0.17489 ( 422) hydrogen bonds : angle 8.62026 ( 1254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 257 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8652 (mt) REVERT: A 51 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8764 (t) REVERT: A 70 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8462 (tt) REVERT: A 96 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8421 (tt) REVERT: A 116 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7361 (mp) REVERT: A 123 MET cc_start: 0.8111 (mtt) cc_final: 0.7886 (mtm) REVERT: A 244 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 247 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8316 (mm) REVERT: B 31 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8687 (mt) REVERT: B 70 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8685 (tt) REVERT: B 96 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8507 (tt) REVERT: B 116 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7383 (mp) REVERT: B 123 MET cc_start: 0.8040 (mtt) cc_final: 0.7767 (mtm) REVERT: B 244 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8465 (mp) REVERT: B 247 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8299 (mm) REVERT: C 170 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: C 176 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8502 (p0) REVERT: C 178 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8876 (tt) REVERT: D 170 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: D 249 ASP cc_start: 0.7663 (t0) cc_final: 0.7359 (p0) REVERT: E 63 ASP cc_start: 0.7917 (t70) cc_final: 0.7700 (t70) REVERT: F 21 ASP cc_start: 0.8688 (p0) cc_final: 0.8117 (p0) REVERT: F 89 ASN cc_start: 0.8389 (t0) cc_final: 0.7831 (t0) outliers start: 128 outliers final: 47 residues processed: 356 average time/residue: 0.0982 time to fit residues: 48.5965 Evaluate side-chains 254 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 190 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 78 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.3980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 50 ASN A 190 GLN B 47 GLN B 50 ASN B 190 GLN C 214 HIS D 175 GLN D 214 HIS E 75 GLN F 75 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097794 restraints weight = 14089.832| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.85 r_work: 0.3075 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9436 Z= 0.142 Angle : 0.727 9.962 12834 Z= 0.345 Chirality : 0.045 0.157 1536 Planarity : 0.006 0.107 1606 Dihedral : 13.155 91.472 1471 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 9.86 % Allowed : 16.60 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.22), residues: 1202 helix: -1.71 (0.18), residues: 652 sheet: -2.16 (0.61), residues: 78 loop : -2.77 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 46 TYR 0.015 0.001 TYR D 81 PHE 0.013 0.001 PHE C 91 TRP 0.018 0.001 TRP E 7 HIS 0.006 0.001 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9436) covalent geometry : angle 0.72721 (12834) hydrogen bonds : bond 0.03860 ( 422) hydrogen bonds : angle 5.93513 ( 1254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 225 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8692 (mt) REVERT: A 51 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8755 (t) REVERT: A 96 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8442 (tt) REVERT: A 116 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7473 (mp) REVERT: A 120 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8215 (pt) REVERT: A 123 MET cc_start: 0.8433 (mtt) cc_final: 0.8221 (mtm) REVERT: A 134 MET cc_start: 0.9046 (tpt) cc_final: 0.8696 (tpt) REVERT: A 198 ASP cc_start: 0.8063 (t0) cc_final: 0.7797 (t0) REVERT: A 216 ILE cc_start: 0.8695 (pp) cc_final: 0.8184 (mm) REVERT: B 31 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8711 (mt) REVERT: B 70 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8709 (tt) REVERT: B 96 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8512 (tt) REVERT: B 120 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8158 (pt) REVERT: B 123 MET cc_start: 0.8395 (mtt) cc_final: 0.8171 (mtm) REVERT: B 134 MET cc_start: 0.8868 (tpt) cc_final: 0.8495 (tpt) REVERT: B 216 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8485 (tp) REVERT: C 105 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7972 (m-40) REVERT: C 172 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.7934 (p90) REVERT: C 207 GLU cc_start: 0.8097 (mp0) cc_final: 0.7797 (mp0) REVERT: D 105 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7930 (m-40) REVERT: D 172 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8110 (p90) REVERT: D 249 ASP cc_start: 0.8246 (t0) cc_final: 0.7560 (p0) REVERT: E 89 ASN cc_start: 0.8756 (t0) cc_final: 0.8008 (t0) REVERT: F 22 GLN cc_start: 0.8446 (pp30) cc_final: 0.7909 (mp10) REVERT: F 66 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8303 (mmtm) REVERT: F 89 ASN cc_start: 0.8731 (t0) cc_final: 0.8163 (t0) outliers start: 98 outliers final: 43 residues processed: 306 average time/residue: 0.0826 time to fit residues: 36.1862 Evaluate side-chains 251 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 194 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 71 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 55 optimal weight: 0.0020 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 ASN D 105 ASN D 175 GLN D 262 HIS E 71 ASN F 75 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.099945 restraints weight = 14199.047| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.85 r_work: 0.3103 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9436 Z= 0.132 Angle : 0.663 9.708 12834 Z= 0.316 Chirality : 0.044 0.147 1536 Planarity : 0.006 0.100 1606 Dihedral : 10.937 87.286 1426 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 7.55 % Allowed : 20.02 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.23), residues: 1202 helix: -1.22 (0.19), residues: 648 sheet: -1.76 (0.55), residues: 94 loop : -2.51 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 97 TYR 0.013 0.001 TYR C 81 PHE 0.011 0.001 PHE A 162 TRP 0.010 0.001 TRP E 7 HIS 0.005 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9436) covalent geometry : angle 0.66345 (12834) hydrogen bonds : bond 0.03502 ( 422) hydrogen bonds : angle 5.52353 ( 1254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 216 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8629 (mt) REVERT: A 96 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8412 (tt) REVERT: A 116 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7296 (mp) REVERT: A 120 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8052 (pt) REVERT: A 216 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8224 (mm) REVERT: B 31 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8648 (mt) REVERT: B 70 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8639 (tt) REVERT: B 96 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8613 (tt) REVERT: B 120 ILE cc_start: 0.8731 (pt) cc_final: 0.8184 (pt) REVERT: B 123 MET cc_start: 0.8389 (mtt) cc_final: 0.8157 (mtm) REVERT: B 216 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8471 (tp) REVERT: C 105 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7912 (m-40) REVERT: C 172 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8138 (p90) REVERT: D 105 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7866 (m-40) REVERT: D 172 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8277 (p90) REVERT: D 249 ASP cc_start: 0.8174 (t0) cc_final: 0.7460 (p0) REVERT: E 7 TRP cc_start: 0.8189 (p90) cc_final: 0.7674 (p-90) REVERT: E 22 GLN cc_start: 0.8271 (pp30) cc_final: 0.7768 (mp10) REVERT: E 66 LYS cc_start: 0.8829 (mmtm) cc_final: 0.8406 (tppt) REVERT: E 89 ASN cc_start: 0.8776 (t0) cc_final: 0.8008 (t0) REVERT: F 7 TRP cc_start: 0.8226 (p90) cc_final: 0.7563 (p-90) REVERT: F 22 GLN cc_start: 0.8305 (pp30) cc_final: 0.7812 (mp10) REVERT: F 68 GLN cc_start: 0.8396 (pp30) cc_final: 0.8037 (pm20) REVERT: F 70 ASN cc_start: 0.6763 (t0) cc_final: 0.6561 (t0) REVERT: F 89 ASN cc_start: 0.8785 (t0) cc_final: 0.8252 (t0) outliers start: 75 outliers final: 41 residues processed: 275 average time/residue: 0.0876 time to fit residues: 34.0224 Evaluate side-chains 246 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 113 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 HIS D 262 HIS F 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.098446 restraints weight = 14226.590| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.90 r_work: 0.3070 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9436 Z= 0.139 Angle : 0.657 11.696 12834 Z= 0.313 Chirality : 0.044 0.142 1536 Planarity : 0.006 0.101 1606 Dihedral : 10.106 85.767 1413 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 8.05 % Allowed : 19.82 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.23), residues: 1202 helix: -1.01 (0.19), residues: 662 sheet: -1.56 (0.55), residues: 94 loop : -2.39 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 46 TYR 0.012 0.001 TYR C 81 PHE 0.012 0.001 PHE B 162 TRP 0.006 0.001 TRP F 7 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9436) covalent geometry : angle 0.65664 (12834) hydrogen bonds : bond 0.03310 ( 422) hydrogen bonds : angle 5.39300 ( 1254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 216 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8620 (mt) REVERT: A 116 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7386 (mp) REVERT: A 120 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8118 (pt) REVERT: A 216 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8267 (mm) REVERT: B 31 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8623 (mt) REVERT: B 84 GLU cc_start: 0.7298 (tm-30) cc_final: 0.7005 (pp20) REVERT: B 96 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8586 (tp) REVERT: B 120 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8210 (pt) REVERT: B 128 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: B 216 ILE cc_start: 0.8714 (pp) cc_final: 0.8211 (mm) REVERT: C 51 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8308 (mp) REVERT: C 105 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7904 (m110) REVERT: C 143 SER cc_start: 0.8591 (t) cc_final: 0.8377 (p) REVERT: C 172 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.7977 (p90) REVERT: D 105 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7873 (m110) REVERT: D 143 SER cc_start: 0.8616 (t) cc_final: 0.8391 (p) REVERT: D 172 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8011 (p90) REVERT: D 249 ASP cc_start: 0.8178 (t0) cc_final: 0.7446 (p0) REVERT: E 7 TRP cc_start: 0.8284 (p90) cc_final: 0.7681 (p-90) REVERT: E 66 LYS cc_start: 0.8866 (mmtm) cc_final: 0.8554 (tppt) REVERT: E 89 ASN cc_start: 0.8787 (t0) cc_final: 0.7984 (t0) REVERT: F 7 TRP cc_start: 0.8201 (p90) cc_final: 0.7542 (p-90) REVERT: F 23 ASP cc_start: 0.8531 (t0) cc_final: 0.8263 (t0) REVERT: F 89 ASN cc_start: 0.8782 (t0) cc_final: 0.8188 (t0) outliers start: 80 outliers final: 52 residues processed: 279 average time/residue: 0.0873 time to fit residues: 34.6672 Evaluate side-chains 266 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 201 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 220 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN F 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.098892 restraints weight = 14235.370| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.90 r_work: 0.3073 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9436 Z= 0.140 Angle : 0.638 9.679 12834 Z= 0.309 Chirality : 0.043 0.148 1536 Planarity : 0.005 0.099 1606 Dihedral : 9.701 86.838 1413 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 7.95 % Allowed : 20.93 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.24), residues: 1202 helix: -0.77 (0.19), residues: 662 sheet: -1.59 (0.53), residues: 94 loop : -2.30 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 46 TYR 0.008 0.001 TYR C 81 PHE 0.013 0.001 PHE B 162 TRP 0.006 0.001 TRP A 195 HIS 0.007 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9436) covalent geometry : angle 0.63829 (12834) hydrogen bonds : bond 0.03265 ( 422) hydrogen bonds : angle 5.27876 ( 1254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 210 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8615 (mt) REVERT: A 98 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7497 (tt0) REVERT: A 116 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7464 (mp) REVERT: A 120 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8183 (pt) REVERT: A 128 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: A 133 GLU cc_start: 0.8506 (tt0) cc_final: 0.8276 (tt0) REVERT: A 197 MET cc_start: 0.6998 (tpp) cc_final: 0.6702 (tpp) REVERT: A 201 ASN cc_start: 0.7825 (m110) cc_final: 0.7549 (m-40) REVERT: A 216 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8304 (mm) REVERT: A 257 MET cc_start: 0.8024 (mtm) cc_final: 0.7694 (mtm) REVERT: B 31 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8606 (mt) REVERT: B 98 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7517 (tt0) REVERT: B 120 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8135 (pt) REVERT: B 128 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: B 216 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8202 (mm) REVERT: C 51 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8314 (mp) REVERT: C 105 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7916 (m110) REVERT: C 143 SER cc_start: 0.8612 (t) cc_final: 0.8382 (p) REVERT: C 172 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.7896 (p90) REVERT: D 105 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.8013 (m110) REVERT: D 143 SER cc_start: 0.8594 (t) cc_final: 0.8379 (p) REVERT: D 172 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.7985 (p90) REVERT: D 249 ASP cc_start: 0.8150 (t0) cc_final: 0.7479 (p0) REVERT: E 7 TRP cc_start: 0.8294 (p90) cc_final: 0.7671 (p-90) REVERT: E 22 GLN cc_start: 0.8361 (pp30) cc_final: 0.7879 (mp10) REVERT: E 89 ASN cc_start: 0.8832 (t0) cc_final: 0.8028 (t0) REVERT: F 7 TRP cc_start: 0.8323 (p90) cc_final: 0.7724 (p-90) REVERT: F 22 GLN cc_start: 0.8319 (pp30) cc_final: 0.7889 (mp10) REVERT: F 23 ASP cc_start: 0.8542 (t0) cc_final: 0.7970 (t0) REVERT: F 89 ASN cc_start: 0.8808 (t0) cc_final: 0.8172 (t0) outliers start: 79 outliers final: 50 residues processed: 273 average time/residue: 0.0862 time to fit residues: 33.7790 Evaluate side-chains 265 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099114 restraints weight = 14224.514| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.92 r_work: 0.3077 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9436 Z= 0.139 Angle : 0.631 9.691 12834 Z= 0.305 Chirality : 0.043 0.166 1536 Planarity : 0.005 0.096 1606 Dihedral : 9.215 77.498 1409 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 7.95 % Allowed : 21.23 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.24), residues: 1202 helix: -0.57 (0.20), residues: 660 sheet: -1.36 (0.56), residues: 84 loop : -2.30 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 46 TYR 0.005 0.001 TYR D 261 PHE 0.012 0.001 PHE B 162 TRP 0.004 0.001 TRP A 195 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9436) covalent geometry : angle 0.63063 (12834) hydrogen bonds : bond 0.03255 ( 422) hydrogen bonds : angle 5.22805 ( 1254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 214 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8539 (mt) REVERT: A 98 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7530 (tt0) REVERT: A 116 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7520 (mp) REVERT: A 120 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8211 (pt) REVERT: A 128 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: A 133 GLU cc_start: 0.8481 (tt0) cc_final: 0.8278 (tt0) REVERT: A 197 MET cc_start: 0.6962 (tpp) cc_final: 0.6687 (tpp) REVERT: A 216 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8279 (mm) REVERT: B 31 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8583 (mt) REVERT: B 98 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7524 (tt0) REVERT: B 120 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8226 (pt) REVERT: B 128 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: B 191 ASN cc_start: 0.7411 (m-40) cc_final: 0.6991 (p0) REVERT: B 216 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8197 (mm) REVERT: C 51 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8251 (mp) REVERT: C 105 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.8002 (m110) REVERT: C 207 GLU cc_start: 0.8242 (mp0) cc_final: 0.7964 (mp0) REVERT: C 262 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6920 (m-70) REVERT: D 105 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.8064 (m110) REVERT: D 143 SER cc_start: 0.8562 (t) cc_final: 0.8361 (p) REVERT: D 249 ASP cc_start: 0.8188 (t0) cc_final: 0.7557 (p0) REVERT: E 7 TRP cc_start: 0.8294 (p90) cc_final: 0.7696 (p-90) REVERT: E 22 GLN cc_start: 0.8327 (pp30) cc_final: 0.7822 (mp10) REVERT: E 66 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8323 (tppt) REVERT: E 89 ASN cc_start: 0.8835 (t0) cc_final: 0.7972 (t0) REVERT: F 7 TRP cc_start: 0.8304 (p90) cc_final: 0.7728 (p-90) REVERT: F 22 GLN cc_start: 0.8200 (pp30) cc_final: 0.7943 (mp10) REVERT: F 23 ASP cc_start: 0.8577 (t0) cc_final: 0.8014 (t0) REVERT: F 75 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7347 (pm20) REVERT: F 89 ASN cc_start: 0.8858 (t0) cc_final: 0.8231 (t0) outliers start: 79 outliers final: 54 residues processed: 276 average time/residue: 0.0966 time to fit residues: 37.2438 Evaluate side-chains 273 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 205 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 29 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.097578 restraints weight = 14252.809| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.91 r_work: 0.3053 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9436 Z= 0.169 Angle : 0.653 9.789 12834 Z= 0.316 Chirality : 0.045 0.182 1536 Planarity : 0.006 0.100 1606 Dihedral : 8.964 71.132 1408 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 7.85 % Allowed : 21.83 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.24), residues: 1202 helix: -0.54 (0.20), residues: 658 sheet: -1.49 (0.53), residues: 94 loop : -2.12 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 46 TYR 0.007 0.001 TYR D 261 PHE 0.014 0.001 PHE B 162 TRP 0.005 0.001 TRP B 195 HIS 0.006 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9436) covalent geometry : angle 0.65262 (12834) hydrogen bonds : bond 0.03337 ( 422) hydrogen bonds : angle 5.27018 ( 1254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 206 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8612 (mt) REVERT: A 98 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7673 (tt0) REVERT: A 116 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.7505 (mp) REVERT: A 120 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8253 (pt) REVERT: A 128 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: A 133 GLU cc_start: 0.8530 (tt0) cc_final: 0.8326 (tt0) REVERT: A 189 MET cc_start: 0.7430 (tpt) cc_final: 0.7209 (tpp) REVERT: A 216 ILE cc_start: 0.8659 (pp) cc_final: 0.8253 (mm) REVERT: A 257 MET cc_start: 0.8136 (mtm) cc_final: 0.7790 (mtm) REVERT: B 31 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8618 (mt) REVERT: B 73 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: B 98 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7633 (tt0) REVERT: B 120 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8211 (pt) REVERT: B 128 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: B 191 ASN cc_start: 0.7415 (m-40) cc_final: 0.6998 (p0) REVERT: B 216 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8253 (mm) REVERT: C 105 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8103 (m110) REVERT: C 207 GLU cc_start: 0.8282 (mp0) cc_final: 0.8012 (mp0) REVERT: C 262 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.6949 (m-70) REVERT: D 105 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8178 (m110) REVERT: D 249 ASP cc_start: 0.8110 (t0) cc_final: 0.7534 (p0) REVERT: E 7 TRP cc_start: 0.8313 (p90) cc_final: 0.7696 (p-90) REVERT: E 66 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8330 (tppt) REVERT: E 89 ASN cc_start: 0.8848 (t0) cc_final: 0.8204 (t0) REVERT: F 23 ASP cc_start: 0.8585 (t0) cc_final: 0.8293 (t0) REVERT: F 66 LYS cc_start: 0.8434 (tppt) cc_final: 0.7948 (tptm) REVERT: F 89 ASN cc_start: 0.8818 (t0) cc_final: 0.8477 (t0) outliers start: 78 outliers final: 53 residues processed: 269 average time/residue: 0.0959 time to fit residues: 36.0429 Evaluate side-chains 266 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 201 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 116 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.121551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099592 restraints weight = 13996.716| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.90 r_work: 0.3084 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9436 Z= 0.132 Angle : 0.634 9.640 12834 Z= 0.306 Chirality : 0.043 0.157 1536 Planarity : 0.005 0.094 1606 Dihedral : 8.600 61.682 1408 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 7.34 % Allowed : 22.33 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.24), residues: 1202 helix: -0.38 (0.20), residues: 656 sheet: -1.04 (0.58), residues: 84 loop : -2.06 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 46 TYR 0.004 0.001 TYR C 108 PHE 0.013 0.001 PHE B 162 TRP 0.004 0.001 TRP B 195 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9436) covalent geometry : angle 0.63441 (12834) hydrogen bonds : bond 0.03224 ( 422) hydrogen bonds : angle 5.17534 ( 1254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 213 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8539 (mt) REVERT: A 98 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7646 (tt0) REVERT: A 116 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7529 (mp) REVERT: A 191 ASN cc_start: 0.7393 (m-40) cc_final: 0.6965 (p0) REVERT: A 197 MET cc_start: 0.7122 (tpp) cc_final: 0.6726 (tpp) REVERT: A 216 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8336 (mm) REVERT: A 257 MET cc_start: 0.8103 (mtm) cc_final: 0.7795 (mtm) REVERT: B 31 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8550 (mt) REVERT: B 73 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: B 98 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7538 (tt0) REVERT: B 120 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8249 (pt) REVERT: B 128 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: B 191 ASN cc_start: 0.7373 (m-40) cc_final: 0.6985 (p0) REVERT: B 216 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8245 (mm) REVERT: C 51 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8292 (mp) REVERT: C 75 MET cc_start: 0.7996 (mtt) cc_final: 0.7703 (mtt) REVERT: C 83 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8960 (p) REVERT: C 105 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8170 (m110) REVERT: C 190 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8029 (mp) REVERT: C 207 GLU cc_start: 0.8196 (mp0) cc_final: 0.7914 (mp0) REVERT: C 235 ASN cc_start: 0.8268 (t0) cc_final: 0.8020 (t0) REVERT: D 172 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7938 (p90) REVERT: D 249 ASP cc_start: 0.8094 (t0) cc_final: 0.7521 (p0) REVERT: E 7 TRP cc_start: 0.8295 (p90) cc_final: 0.7661 (p-90) REVERT: E 22 GLN cc_start: 0.8265 (pp30) cc_final: 0.7840 (mp10) REVERT: E 66 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8263 (tppt) REVERT: E 89 ASN cc_start: 0.8854 (t0) cc_final: 0.8203 (t0) REVERT: F 22 GLN cc_start: 0.8199 (pp30) cc_final: 0.7952 (mp10) REVERT: F 89 ASN cc_start: 0.8857 (t0) cc_final: 0.8217 (t0) outliers start: 73 outliers final: 54 residues processed: 269 average time/residue: 0.0984 time to fit residues: 36.7475 Evaluate side-chains 270 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 203 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 57 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 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 = 0.3554 r_free = 0.3554 target = 0.125580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103090 restraints weight = 13602.308| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.93 r_work: 0.3089 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9436 Z= 0.138 Angle : 0.638 9.727 12834 Z= 0.309 Chirality : 0.043 0.166 1536 Planarity : 0.005 0.094 1606 Dihedral : 8.207 60.556 1404 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 7.65 % Allowed : 22.64 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.24), residues: 1202 helix: -0.30 (0.20), residues: 656 sheet: -0.85 (0.60), residues: 84 loop : -2.00 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 46 TYR 0.004 0.001 TYR B 75 PHE 0.013 0.001 PHE B 162 TRP 0.004 0.001 TRP B 195 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9436) covalent geometry : angle 0.63813 (12834) hydrogen bonds : bond 0.03247 ( 422) hydrogen bonds : angle 5.16912 ( 1254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 207 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8524 (mt) REVERT: A 98 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7594 (tt0) REVERT: A 116 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7545 (mp) REVERT: A 191 ASN cc_start: 0.7425 (m-40) cc_final: 0.6993 (p0) REVERT: A 197 MET cc_start: 0.7089 (tpp) cc_final: 0.6681 (tpp) REVERT: A 216 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8304 (mm) REVERT: A 257 MET cc_start: 0.8160 (mtm) cc_final: 0.7862 (mtm) REVERT: B 31 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8564 (mt) REVERT: B 73 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: B 98 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7579 (tt0) REVERT: B 128 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: B 191 ASN cc_start: 0.7397 (m-40) cc_final: 0.7004 (p0) REVERT: B 216 ILE cc_start: 0.8678 (pp) cc_final: 0.8242 (mm) REVERT: C 12 ARG cc_start: 0.7999 (mmt90) cc_final: 0.7789 (mmt90) REVERT: C 51 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8265 (mp) REVERT: C 75 MET cc_start: 0.7953 (mtt) cc_final: 0.7643 (mtt) REVERT: C 83 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8940 (p) REVERT: C 105 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8153 (m110) REVERT: C 190 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8009 (mp) REVERT: C 207 GLU cc_start: 0.8196 (mp0) cc_final: 0.7935 (mp0) REVERT: C 235 ASN cc_start: 0.8299 (t0) cc_final: 0.8029 (t0) REVERT: D 83 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8975 (p) REVERT: D 190 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8003 (mp) REVERT: D 249 ASP cc_start: 0.8209 (t0) cc_final: 0.7571 (p0) REVERT: E 7 TRP cc_start: 0.8246 (p90) cc_final: 0.7630 (p-90) REVERT: E 22 GLN cc_start: 0.8113 (pp30) cc_final: 0.7825 (mp10) REVERT: E 66 LYS cc_start: 0.8668 (mmtm) cc_final: 0.8179 (tppt) REVERT: F 89 ASN cc_start: 0.8800 (t0) cc_final: 0.8141 (t0) outliers start: 76 outliers final: 58 residues processed: 266 average time/residue: 0.0946 time to fit residues: 35.3820 Evaluate side-chains 268 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 198 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.100971 restraints weight = 13746.120| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.94 r_work: 0.3093 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9436 Z= 0.175 Angle : 0.672 9.741 12834 Z= 0.325 Chirality : 0.044 0.167 1536 Planarity : 0.005 0.096 1606 Dihedral : 8.225 61.242 1404 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 7.34 % Allowed : 22.84 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.24), residues: 1202 helix: -0.34 (0.20), residues: 654 sheet: -0.87 (0.60), residues: 84 loop : -1.99 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 46 TYR 0.007 0.001 TYR B 75 PHE 0.015 0.001 PHE B 162 TRP 0.005 0.001 TRP A 195 HIS 0.004 0.001 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 9436) covalent geometry : angle 0.67247 (12834) hydrogen bonds : bond 0.03394 ( 422) hydrogen bonds : angle 5.24896 ( 1254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 198 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8582 (mt) REVERT: A 98 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7607 (tt0) REVERT: A 116 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7481 (mp) REVERT: A 120 ILE cc_start: 0.8741 (pt) cc_final: 0.8188 (pt) REVERT: A 216 ILE cc_start: 0.8707 (pp) cc_final: 0.8307 (mm) REVERT: A 257 MET cc_start: 0.8244 (mtm) cc_final: 0.7937 (mtm) REVERT: B 31 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8590 (mt) REVERT: B 73 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: B 98 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7623 (tt0) REVERT: B 120 ILE cc_start: 0.8770 (pt) cc_final: 0.8262 (pt) REVERT: B 128 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: B 191 ASN cc_start: 0.7425 (m-40) cc_final: 0.7015 (p0) REVERT: B 197 MET cc_start: 0.6716 (tpp) cc_final: 0.6308 (tpp) REVERT: B 216 ILE cc_start: 0.8685 (pp) cc_final: 0.8255 (mm) REVERT: C 51 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8309 (mp) REVERT: C 75 MET cc_start: 0.7985 (mtt) cc_final: 0.7687 (mtt) REVERT: C 83 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8978 (p) REVERT: C 105 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8142 (m110) REVERT: C 190 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.7928 (mp) REVERT: C 207 GLU cc_start: 0.8262 (mp0) cc_final: 0.7987 (mp0) REVERT: C 235 ASN cc_start: 0.8402 (t0) cc_final: 0.8096 (t0) REVERT: D 81 TYR cc_start: 0.7896 (m-80) cc_final: 0.7543 (t80) REVERT: D 83 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.9026 (p) REVERT: D 190 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.7923 (mp) REVERT: D 249 ASP cc_start: 0.8184 (t0) cc_final: 0.7575 (p0) REVERT: E 7 TRP cc_start: 0.8272 (p90) cc_final: 0.7608 (p-90) REVERT: E 22 GLN cc_start: 0.8156 (pp30) cc_final: 0.7840 (mp10) REVERT: E 23 ASP cc_start: 0.8608 (t0) cc_final: 0.7980 (t0) REVERT: E 66 LYS cc_start: 0.8754 (mmtm) cc_final: 0.8234 (tppt) REVERT: F 89 ASN cc_start: 0.8743 (t0) cc_final: 0.8370 (t0) outliers start: 73 outliers final: 58 residues processed: 257 average time/residue: 0.0948 time to fit residues: 34.2770 Evaluate side-chains 263 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 194 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 71 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 98 optimal weight: 0.0040 chunk 34 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.104121 restraints weight = 13498.168| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.93 r_work: 0.3106 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9436 Z= 0.130 Angle : 0.655 9.735 12834 Z= 0.315 Chirality : 0.043 0.158 1536 Planarity : 0.005 0.089 1606 Dihedral : 8.020 59.505 1404 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 7.34 % Allowed : 23.24 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.25), residues: 1202 helix: -0.17 (0.20), residues: 654 sheet: -0.76 (0.61), residues: 84 loop : -1.96 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 46 TYR 0.003 0.001 TYR B 75 PHE 0.013 0.001 PHE B 162 TRP 0.005 0.001 TRP A 195 HIS 0.003 0.001 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9436) covalent geometry : angle 0.65479 (12834) hydrogen bonds : bond 0.03220 ( 422) hydrogen bonds : angle 5.11896 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2316.09 seconds wall clock time: 40 minutes 18.95 seconds (2418.95 seconds total)