Starting phenix.real_space_refine on Thu Aug 6 03:47:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vjb_65109/08_2026/9vjb_65109.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vjb_65109/08_2026/9vjb_65109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vjb_65109/08_2026/9vjb_65109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vjb_65109/08_2026/9vjb_65109.map" model { file = "/net/cci-nas-00/data/ceres_data/9vjb_65109/08_2026/9vjb_65109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vjb_65109/08_2026/9vjb_65109.cif" } resolution = 3.76 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= 0.002 sd= 0.017 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 50 5.49 5 S 41 5.16 5 C 8289 2.51 5 N 2133 2.21 5 O 2596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13115 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1783 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 215} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1791 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "C" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1791 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "D" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1791 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 215} Chain: "I" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2359 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain: "J" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2350 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain: "X" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 500 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "Y" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 525 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "N" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 219 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.99, per 1000 atoms: 0.23 Number of scatterers: 13115 At special positions: 0 Unit cell: (99.724, 115.568, 149.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 41 16.00 P 50 15.00 O 2596 8.00 N 2133 7.00 C 8289 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: 0.97 Conformation dependent library (CDL) restraints added in 572.9 milliseconds 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2838 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 16 sheets defined 48.5% alpha, 12.2% beta 25 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 72 through 89 removed outlier: 3.580A pdb=" N LEU A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 113 removed outlier: 3.649A pdb=" N GLU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 143 through 158 Processing helix chain 'A' and resid 168 through 173 removed outlier: 4.131A pdb=" N TYR A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 173' Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'B' and resid 24 through 36 Processing helix chain 'B' and resid 72 through 89 Processing helix chain 'B' and resid 91 through 114 Processing helix chain 'B' and resid 125 through 134 removed outlier: 3.512A pdb=" N GLY B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 158 removed outlier: 4.200A pdb=" N GLU B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'C' and resid 24 through 37 Processing helix chain 'C' and resid 72 through 90 removed outlier: 4.144A pdb=" N LYS C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 114 removed outlier: 4.072A pdb=" N LYS C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 143 through 158 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.904A pdb=" N TYR C 172 " --> pdb=" O ALA C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 174 through 189 Processing helix chain 'D' and resid 24 through 37 Processing helix chain 'D' and resid 72 through 90 removed outlier: 3.790A pdb=" N LYS D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 115 removed outlier: 3.578A pdb=" N LYS D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 133 Processing helix chain 'D' and resid 143 through 158 Processing helix chain 'D' and resid 174 through 189 Processing helix chain 'I' and resid 51 through 60 Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'I' and resid 89 through 94 Processing helix chain 'I' and resid 98 through 123 Processing helix chain 'I' and resid 125 through 138 removed outlier: 3.623A pdb=" N ALA I 129 " --> pdb=" O TYR I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 161 Processing helix chain 'I' and resid 170 through 194 removed outlier: 3.600A pdb=" N ALA I 174 " --> pdb=" O ASN I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 217 Processing helix chain 'I' and resid 218 through 221 Processing helix chain 'I' and resid 222 through 230 removed outlier: 3.791A pdb=" N ASP I 226 " --> pdb=" O ARG I 222 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE I 228 " --> pdb=" O LEU I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 231 through 233 No H-bonds generated for 'chain 'I' and resid 231 through 233' Processing helix chain 'I' and resid 236 through 245 Processing helix chain 'I' and resid 260 through 277 Processing helix chain 'J' and resid 51 through 60 Processing helix chain 'J' and resid 86 through 95 Processing helix chain 'J' and resid 97 through 122 removed outlier: 3.754A pdb=" N GLN J 122 " --> pdb=" O LEU J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 138 removed outlier: 4.338A pdb=" N ALA J 131 " --> pdb=" O GLN J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 160 Processing helix chain 'J' and resid 170 through 194 removed outlier: 3.584A pdb=" N ALA J 174 " --> pdb=" O ASN J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 217 Processing helix chain 'J' and resid 218 through 220 No H-bonds generated for 'chain 'J' and resid 218 through 220' Processing helix chain 'J' and resid 221 through 232 removed outlier: 3.960A pdb=" N VAL J 225 " --> pdb=" O PHE J 221 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE J 228 " --> pdb=" O LEU J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 245 Processing helix chain 'J' and resid 246 through 249 Processing helix chain 'J' and resid 260 through 277 Processing helix chain 'N' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 3.932A pdb=" N VAL A 3 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A 12 " --> pdb=" O VAL A 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 62 removed outlier: 5.804A pdb=" N LEU A 164 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU A 195 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE A 166 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 18 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N TYR A 206 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 19 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU A 208 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR A 21 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 217 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.552A pdb=" N LYS D 136 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.862A pdb=" N ILE B 12 " --> pdb=" O VAL B 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.720A pdb=" N PHE B 60 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ILE B 167 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL B 62 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 164 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU B 195 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE B 166 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 217 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 207 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 215 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AA7, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AA8, first strand: chain 'C' and resid 2 through 3 removed outlier: 3.559A pdb=" N VAL C 3 " --> pdb=" O ILE C 12 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.349A pdb=" N LEU C 164 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU C 195 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE C 166 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR C 18 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 22 " --> pdb=" O GLU C 196 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N ALA C 17 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N TYR C 206 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE C 19 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU C 208 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR C 21 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 47 through 48 Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.692A pdb=" N LYS D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 59 through 62 removed outlier: 6.949A pdb=" N PHE D 60 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE D 167 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL D 62 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU D 164 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU D 195 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE D 166 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE D 204 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE D 19 " --> pdb=" O PHE D 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 4 through 7 removed outlier: 7.311A pdb=" N ARG I 4 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU I 40 " --> pdb=" O ARG I 4 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL I 6 " --> pdb=" O LEU I 40 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU I 63 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL I 64 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS I 76 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE I 66 " --> pdb=" O ILE I 74 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE J 66 " --> pdb=" O ILE J 74 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS J 76 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL J 64 " --> pdb=" O LYS J 76 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG J 4 " --> pdb=" O VAL J 39 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N LEU J 41 " --> pdb=" O ARG J 4 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL J 6 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N THR J 5 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU N 106 " --> pdb=" O THR J 5 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL J 7 " --> pdb=" O LEU N 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 29 through 33 removed outlier: 6.732A pdb=" N TYR I 16 " --> pdb=" O THR I 50 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TYR J 16 " --> pdb=" O THR J 50 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER J 15 " --> pdb=" O VAL J 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 252 through 254 removed outlier: 3.558A pdb=" N MET I 259 " --> pdb=" O TYR I 252 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 252 through 253 591 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3062 1.33 - 1.45: 2916 1.45 - 1.58: 7289 1.58 - 1.70: 98 1.70 - 1.82: 74 Bond restraints: 13439 Sorted by residual: bond pdb=" C GLU J 219 " pdb=" N PRO J 220 " ideal model delta sigma weight residual 1.334 1.377 -0.043 8.40e-03 1.42e+04 2.62e+01 bond pdb=" C3' DT X 18 " pdb=" C2' DT X 18 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DT X 21 " pdb=" C2' DT X 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.52e+00 bond pdb=" N PHE J 260 " pdb=" CA PHE J 260 " ideal model delta sigma weight residual 1.454 1.492 -0.039 1.34e-02 5.57e+03 8.32e+00 bond pdb=" CG HIS N 89 " pdb=" CD2 HIS N 89 " ideal model delta sigma weight residual 1.354 1.325 0.029 1.10e-02 8.26e+03 6.91e+00 ... (remaining 13434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 18158 3.59 - 7.18: 172 7.18 - 10.78: 30 10.78 - 14.37: 11 14.37 - 17.96: 1 Bond angle restraints: 18372 Sorted by residual: angle pdb=" CA LYS D 160 " pdb=" CB LYS D 160 " pdb=" CG LYS D 160 " ideal model delta sigma weight residual 114.10 127.02 -12.92 2.00e+00 2.50e-01 4.17e+01 angle pdb=" C ASP B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 angle pdb=" N ILE B 65 " pdb=" CA ILE B 65 " pdb=" C ILE B 65 " ideal model delta sigma weight residual 112.29 107.20 5.09 9.40e-01 1.13e+00 2.94e+01 angle pdb=" C ASN J 18 " pdb=" N ASN J 19 " pdb=" CA ASN J 19 " ideal model delta sigma weight residual 122.46 129.90 -7.44 1.41e+00 5.03e-01 2.78e+01 angle pdb=" N PHE N 82 " pdb=" CA PHE N 82 " pdb=" C PHE N 82 " ideal model delta sigma weight residual 111.28 105.59 5.69 1.09e+00 8.42e-01 2.72e+01 ... (remaining 18367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6349 17.84 - 35.67: 1074 35.67 - 53.51: 447 53.51 - 71.35: 143 71.35 - 89.18: 25 Dihedral angle restraints: 8038 sinusoidal: 3663 harmonic: 4375 Sorted by residual: dihedral pdb=" CD ARG N 102 " pdb=" NE ARG N 102 " pdb=" CZ ARG N 102 " pdb=" NH1 ARG N 102 " ideal model delta sinusoidal sigma weight residual 0.00 -72.75 72.75 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CA PRO A 56 " pdb=" C PRO A 56 " pdb=" N THR A 57 " pdb=" CA THR A 57 " ideal model delta harmonic sigma weight residual 180.00 150.03 29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LYS B 90 " pdb=" C LYS B 90 " pdb=" N PRO B 91 " pdb=" CA PRO B 91 " ideal model delta harmonic sigma weight residual 180.00 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 8035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1952 0.097 - 0.194: 154 0.194 - 0.291: 13 0.291 - 0.388: 0 0.388 - 0.485: 1 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CG LEU B 107 " pdb=" CB LEU B 107 " pdb=" CD1 LEU B 107 " pdb=" CD2 LEU B 107 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" CB ILE D 97 " pdb=" CA ILE D 97 " pdb=" CG1 ILE D 97 " pdb=" CG2 ILE D 97 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE B 65 " pdb=" CA ILE B 65 " pdb=" CG1 ILE B 65 " pdb=" CG2 ILE B 65 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2117 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 102 " -1.035 9.50e-02 1.11e+02 4.64e-01 1.30e+02 pdb=" NE ARG N 102 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG N 102 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG N 102 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG N 102 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 189 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASN B 189 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN B 189 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL B 190 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 23 " 0.027 2.00e-02 2.50e+03 2.69e-02 1.26e+01 pdb=" CG PHE J 23 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE J 23 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE J 23 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE J 23 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE J 23 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE J 23 " 0.009 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 12 2.01 - 2.73: 853 2.73 - 3.45: 18242 3.45 - 4.18: 31381 4.18 - 4.90: 53201 Nonbonded interactions: 103689 Sorted by model distance: nonbonded pdb=" OD1 ASN J 18 " pdb=" OE2 GLU N 91 " model vdw 1.285 3.040 nonbonded pdb=" OD2 ASP B 118 " pdb=" OE2 GLU C 146 " model vdw 1.344 3.040 nonbonded pdb=" OG SER J 35 " pdb=" CG ASN N 94 " model vdw 1.558 3.270 nonbonded pdb=" OD1 ASP C 142 " pdb=" OE1 GLU C 146 " model vdw 1.585 3.040 nonbonded pdb=" OE1 GLU B 128 " pdb=" O ALA C 132 " model vdw 1.631 3.040 ... (remaining 103684 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 301) selection = (chain 'B' and (resid 1 through 152 or (resid 153 and (name N or name CA or name \ C or name O or name CB )) or resid 154 through 176 or (resid 177 and (name N or \ name CA or name C or name O or name CB )) or resid 178 through 301)) selection = (chain 'C' and (resid 1 through 152 or (resid 153 and (name N or name CA or name \ C or name O or name CB )) or resid 154 through 176 or (resid 177 and (name N or \ name CA or name C or name O or name CB )) or resid 178 through 301)) selection = (chain 'D' and (resid 1 through 152 or (resid 153 and (name N or name CA or name \ C or name O or name CB )) or resid 154 through 176 or (resid 177 and (name N or \ name CA or name C or name O or name CB )) or resid 178 through 301)) } ncs_group { reference = (chain 'I' and resid 1 through 287) selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.390 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.005 0.053 13439 Z= 0.306 Angle : 1.040 17.959 18372 Z= 0.600 Chirality : 0.055 0.485 2120 Planarity : 0.012 0.464 2160 Dihedral : 21.828 89.182 5200 Min Nonbonded Distance : 1.285 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.37 % Favored : 95.15 % Rotamer: Outliers : 4.04 % Allowed : 33.88 % Favored : 62.08 % 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: -2.31 (0.19), residues: 1465 helix: -1.14 (0.17), residues: 673 sheet: -1.10 (0.42), residues: 157 loop : -1.99 (0.21), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 92 TYR 0.028 0.002 TYR A 206 PHE 0.062 0.003 PHE J 23 TRP 0.038 0.003 TRP I 3 HIS 0.015 0.002 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.31 (13439) covalent geometry : angle 1.04037 / 0.60 (18372) hydrogen bonds : bond 0.15082 / 10.36 ( 641) hydrogen bonds : angle 6.02957 / 4.25 ( 1807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 317 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8330 (pptt) REVERT: A 138 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5639 (tm-30) REVERT: A 149 MET cc_start: 0.8383 (mmm) cc_final: 0.8100 (mmp) REVERT: A 164 LEU cc_start: 0.8321 (tp) cc_final: 0.7917 (mp) REVERT: A 206 TYR cc_start: 0.6942 (m-10) cc_final: 0.5562 (m-80) REVERT: C 107 LEU cc_start: 0.9127 (mt) cc_final: 0.8840 (mt) REVERT: C 137 ILE cc_start: 0.8163 (mt) cc_final: 0.7598 (mt) REVERT: D 42 ASN cc_start: 0.7623 (m110) cc_final: 0.6652 (m-40) REVERT: D 150 GLU cc_start: 0.8155 (tt0) cc_final: 0.7938 (tt0) REVERT: I 39 VAL cc_start: 0.9357 (t) cc_final: 0.8955 (t) REVERT: J 190 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8004 (mm-30) outliers start: 54 outliers final: 17 residues processed: 361 average time/residue: 0.1088 time to fit residues: 57.7189 Evaluate side-chains 193 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 215 SER Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 168 ASN A 201 GLN A 202 ASN B 115 HIS B 168 ASN C 179 GLN D 106 GLN D 188 ASN ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 HIS J 258 GLN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.098220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.068137 restraints weight = 43319.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.069988 restraints weight = 23998.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071283 restraints weight = 16299.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.072204 restraints weight = 12453.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.072622 restraints weight = 10346.906| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13439 Z= 0.232 Angle : 0.729 8.340 18372 Z= 0.391 Chirality : 0.045 0.238 2120 Planarity : 0.005 0.096 2160 Dihedral : 18.502 89.944 2221 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.89 % Favored : 95.84 % Rotamer: Outliers : 6.66 % Allowed : 30.07 % Favored : 63.28 % 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: -1.01 (0.21), residues: 1465 helix: 0.35 (0.19), residues: 688 sheet: -0.72 (0.46), residues: 139 loop : -1.78 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG C 198 TYR 0.021 0.002 TYR A 206 PHE 0.041 0.002 PHE D 145 TRP 0.033 0.003 TRP I 3 HIS 0.012 0.002 HIS J 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (13439) covalent geometry : angle 0.72884 / 0.39 (18372) hydrogen bonds : bond 0.05082 / 3.40 ( 641) hydrogen bonds : angle 4.61025 / 3.24 ( 1807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 165 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8981 (tpp) cc_final: 0.8772 (tpp) REVERT: A 138 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6017 (pt0) REVERT: A 142 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: A 162 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8391 (mmmm) REVERT: A 164 LEU cc_start: 0.8780 (tp) cc_final: 0.8347 (mp) REVERT: B 44 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8632 (pt) REVERT: B 115 HIS cc_start: 0.8312 (OUTLIER) cc_final: 0.7778 (t-90) REVERT: B 213 TYR cc_start: 0.8540 (m-80) cc_final: 0.8322 (m-80) REVERT: D 96 MET cc_start: 0.9004 (tpp) cc_final: 0.8702 (tpp) REVERT: D 150 GLU cc_start: 0.8923 (tt0) cc_final: 0.8662 (tt0) REVERT: D 196 GLU cc_start: 0.7400 (tt0) cc_final: 0.7054 (mt-10) REVERT: I 24 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8018 (tmtt) REVERT: I 155 TYR cc_start: 0.8509 (t80) cc_final: 0.8035 (t80) REVERT: I 240 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.9075 (mpp) REVERT: I 249 MET cc_start: 0.8902 (ptp) cc_final: 0.8675 (ptp) REVERT: J 146 ASN cc_start: 0.9469 (t0) cc_final: 0.9198 (t0) REVERT: J 190 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8253 (mm-30) REVERT: J 240 MET cc_start: 0.9110 (mtm) cc_final: 0.8514 (mtm) outliers start: 89 outliers final: 41 residues processed: 242 average time/residue: 0.0915 time to fit residues: 33.5109 Evaluate side-chains 194 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 190 GLU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 54 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 202 ASN B 168 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN C 30 HIS J 9 ASN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.087536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.054988 restraints weight = 43584.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.056881 restraints weight = 24305.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.058110 restraints weight = 16608.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.058992 restraints weight = 12844.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.059515 restraints weight = 10811.661| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13439 Z= 0.168 Angle : 0.638 6.810 18372 Z= 0.345 Chirality : 0.043 0.312 2120 Planarity : 0.004 0.050 2160 Dihedral : 18.356 89.457 2210 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.30 % Favored : 95.56 % Rotamer: Outliers : 5.01 % Allowed : 29.54 % Favored : 65.45 % 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: -0.53 (0.22), residues: 1465 helix: 0.89 (0.20), residues: 686 sheet: -1.22 (0.43), residues: 161 loop : -1.52 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 4 TYR 0.018 0.002 TYR A 216 PHE 0.021 0.002 PHE N 82 TRP 0.035 0.003 TRP I 3 HIS 0.009 0.001 HIS J 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (13439) covalent geometry : angle 0.63848 / 0.34 (18372) hydrogen bonds : bond 0.04458 / 2.98 ( 641) hydrogen bonds : angle 4.32063 / 3.03 ( 1807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 149 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8544 (mt) REVERT: A 142 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: A 162 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8416 (mmmm) REVERT: A 164 LEU cc_start: 0.8756 (tp) cc_final: 0.8381 (mp) REVERT: B 44 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8636 (pt) REVERT: B 213 TYR cc_start: 0.8574 (m-80) cc_final: 0.8288 (m-80) REVERT: B 216 TYR cc_start: 0.9177 (t80) cc_final: 0.8738 (t80) REVERT: D 96 MET cc_start: 0.9043 (tpp) cc_final: 0.8699 (tpp) REVERT: D 150 GLU cc_start: 0.8967 (tt0) cc_final: 0.8663 (tt0) REVERT: D 196 GLU cc_start: 0.7303 (tt0) cc_final: 0.6899 (mt-10) REVERT: I 24 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8060 (tmtt) REVERT: I 249 MET cc_start: 0.8891 (ptp) cc_final: 0.8651 (ptp) REVERT: J 146 ASN cc_start: 0.9550 (t0) cc_final: 0.9253 (t0) REVERT: J 190 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: J 240 MET cc_start: 0.9154 (mtm) cc_final: 0.8702 (mtp) REVERT: J 245 PHE cc_start: 0.9078 (m-80) cc_final: 0.8712 (m-80) outliers start: 67 outliers final: 32 residues processed: 204 average time/residue: 0.0939 time to fit residues: 29.2283 Evaluate side-chains 171 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 190 GLU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 259 MET Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 57 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN B 115 HIS B 168 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 HIS J 277 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.093864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.063646 restraints weight = 44835.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.065321 restraints weight = 25448.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.066453 restraints weight = 17576.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.067328 restraints weight = 13801.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.067982 restraints weight = 11392.220| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 13439 Z= 0.341 Angle : 0.747 8.224 18372 Z= 0.394 Chirality : 0.045 0.230 2120 Planarity : 0.004 0.047 2160 Dihedral : 18.415 88.724 2202 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.91 % Favored : 94.95 % Rotamer: Outliers : 5.91 % Allowed : 29.24 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.44 (0.22), residues: 1465 helix: 1.12 (0.20), residues: 682 sheet: -1.33 (0.47), residues: 133 loop : -1.62 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 203 TYR 0.026 0.002 TYR A 216 PHE 0.021 0.002 PHE B 5 TRP 0.036 0.004 TRP I 3 HIS 0.008 0.002 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.34 (13439) covalent geometry : angle 0.74717 / 0.39 (18372) hydrogen bonds : bond 0.04870 / 3.28 ( 641) hydrogen bonds : angle 4.53220 / 3.18 ( 1807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 135 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 142 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8236 (m-30) REVERT: B 44 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8780 (pt) REVERT: B 115 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.7752 (t-90) REVERT: B 213 TYR cc_start: 0.8664 (m-80) cc_final: 0.8425 (m-10) REVERT: D 50 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8302 (tp-100) REVERT: D 96 MET cc_start: 0.9074 (tpp) cc_final: 0.8765 (tpp) REVERT: D 150 GLU cc_start: 0.8994 (tt0) cc_final: 0.8752 (tt0) REVERT: D 196 GLU cc_start: 0.7398 (tt0) cc_final: 0.6962 (mt-10) REVERT: I 24 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.7962 (tmtt) REVERT: I 159 LEU cc_start: 0.8521 (tp) cc_final: 0.8280 (tp) REVERT: I 242 ARG cc_start: 0.9144 (tpm170) cc_final: 0.8938 (tpm170) REVERT: I 249 MET cc_start: 0.8924 (ptp) cc_final: 0.8706 (ptp) REVERT: I 259 MET cc_start: 0.8488 (pmm) cc_final: 0.7406 (pmm) REVERT: J 146 ASN cc_start: 0.9670 (t0) cc_final: 0.9468 (t0) REVERT: J 190 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8851 (mm-30) REVERT: J 276 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8714 (tp) outliers start: 79 outliers final: 47 residues processed: 201 average time/residue: 0.0838 time to fit residues: 26.2624 Evaluate side-chains 179 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 198 THR Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 56 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN A 202 ASN B 115 HIS B 168 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.092640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.062225 restraints weight = 44782.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.063990 restraints weight = 24495.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.065243 restraints weight = 16587.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.066119 restraints weight = 12641.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.066613 restraints weight = 10510.994| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13439 Z= 0.142 Angle : 0.611 8.293 18372 Z= 0.326 Chirality : 0.042 0.200 2120 Planarity : 0.003 0.038 2160 Dihedral : 18.372 88.926 2199 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.49 % Rotamer: Outliers : 4.19 % Allowed : 30.07 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.22 (0.22), residues: 1465 helix: 1.27 (0.20), residues: 686 sheet: -0.86 (0.47), residues: 145 loop : -1.58 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 203 TYR 0.031 0.001 TYR A 216 PHE 0.024 0.001 PHE A 204 TRP 0.035 0.003 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (13439) covalent geometry : angle 0.61145 / 0.33 (18372) hydrogen bonds : bond 0.04032 / 2.72 ( 641) hydrogen bonds : angle 4.15975 / 2.88 ( 1807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 143 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.9027 (tpp) cc_final: 0.8757 (tpp) REVERT: A 110 TYR cc_start: 0.8825 (t80) cc_final: 0.8476 (t80) REVERT: A 113 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8252 (mt) REVERT: A 142 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: B 1 MET cc_start: 0.7672 (mmp) cc_final: 0.7416 (mmp) REVERT: B 36 TYR cc_start: 0.8994 (m-80) cc_final: 0.8726 (m-80) REVERT: B 44 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8615 (pt) REVERT: B 149 MET cc_start: 0.9284 (mmm) cc_final: 0.9008 (mmm) REVERT: B 213 TYR cc_start: 0.8638 (m-80) cc_final: 0.8386 (m-10) REVERT: B 216 TYR cc_start: 0.9183 (t80) cc_final: 0.8767 (t80) REVERT: D 96 MET cc_start: 0.9073 (tpp) cc_final: 0.8719 (tpp) REVERT: D 150 GLU cc_start: 0.9021 (tt0) cc_final: 0.8788 (tt0) REVERT: D 196 GLU cc_start: 0.7275 (tt0) cc_final: 0.6886 (mt-10) REVERT: I 24 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.7923 (tmtt) REVERT: I 135 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8196 (pmm) REVERT: I 159 LEU cc_start: 0.8511 (tp) cc_final: 0.8304 (tp) REVERT: I 242 ARG cc_start: 0.9186 (tpm170) cc_final: 0.8962 (tpm170) REVERT: I 249 MET cc_start: 0.8902 (ptp) cc_final: 0.8663 (ptp) REVERT: I 259 MET cc_start: 0.8455 (pmm) cc_final: 0.7421 (pmm) REVERT: J 41 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8865 (tt) REVERT: J 190 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8208 (mm-30) REVERT: J 276 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8717 (tp) outliers start: 56 outliers final: 36 residues processed: 188 average time/residue: 0.0805 time to fit residues: 23.6933 Evaluate side-chains 180 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 113 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 102 optimal weight: 10.0000 chunk 141 optimal weight: 50.0000 chunk 124 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN B 168 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS J 9 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.093186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.063041 restraints weight = 43904.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.064780 restraints weight = 23871.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.065976 restraints weight = 16207.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.066889 restraints weight = 12526.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.067477 restraints weight = 10279.874| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13439 Z= 0.139 Angle : 0.592 8.101 18372 Z= 0.317 Chirality : 0.041 0.179 2120 Planarity : 0.003 0.039 2160 Dihedral : 18.337 89.701 2199 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.49 % Rotamer: Outliers : 4.26 % Allowed : 30.22 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.10 (0.22), residues: 1465 helix: 1.37 (0.20), residues: 684 sheet: -1.14 (0.49), residues: 133 loop : -1.44 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 222 TYR 0.028 0.001 TYR A 216 PHE 0.023 0.001 PHE A 204 TRP 0.042 0.003 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (13439) covalent geometry : angle 0.59183 / 0.32 (18372) hydrogen bonds : bond 0.03896 / 2.63 ( 641) hydrogen bonds : angle 4.06475 / 2.82 ( 1807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 142 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 TYR cc_start: 0.8994 (m-80) cc_final: 0.8633 (m-80) REVERT: B 44 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8600 (pt) REVERT: B 149 MET cc_start: 0.9293 (mmm) cc_final: 0.8996 (mmm) REVERT: B 213 TYR cc_start: 0.8633 (m-80) cc_final: 0.8346 (m-80) REVERT: B 216 TYR cc_start: 0.9183 (t80) cc_final: 0.8776 (t80) REVERT: D 96 MET cc_start: 0.9077 (tpp) cc_final: 0.8717 (tpp) REVERT: D 150 GLU cc_start: 0.8996 (tt0) cc_final: 0.8771 (tt0) REVERT: D 196 GLU cc_start: 0.7214 (tt0) cc_final: 0.6880 (mt-10) REVERT: I 135 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8168 (pmm) REVERT: I 242 ARG cc_start: 0.9179 (tpm170) cc_final: 0.8942 (tpm170) REVERT: I 249 MET cc_start: 0.8937 (ptp) cc_final: 0.8716 (ptp) REVERT: I 259 MET cc_start: 0.8412 (pmm) cc_final: 0.7337 (pmm) REVERT: J 41 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8883 (tt) REVERT: J 190 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8240 (tp30) REVERT: J 276 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8685 (tp) outliers start: 57 outliers final: 37 residues processed: 188 average time/residue: 0.0968 time to fit residues: 27.8238 Evaluate side-chains 178 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 259 MET Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 132 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN A 202 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 GLN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.089819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.059659 restraints weight = 45453.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.061341 restraints weight = 25329.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.062471 restraints weight = 17253.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.063237 restraints weight = 13302.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.063685 restraints weight = 11190.724| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 13439 Z= 0.346 Angle : 0.733 8.335 18372 Z= 0.385 Chirality : 0.044 0.221 2120 Planarity : 0.004 0.041 2160 Dihedral : 18.459 88.226 2197 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.67 % Favored : 94.20 % Rotamer: Outliers : 5.09 % Allowed : 30.07 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.39 (0.22), residues: 1465 helix: 1.19 (0.20), residues: 685 sheet: -1.43 (0.48), residues: 137 loop : -1.62 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 203 TYR 0.028 0.002 TYR A 216 PHE 0.022 0.002 PHE A 204 TRP 0.029 0.003 TRP I 3 HIS 0.008 0.002 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00776 / 0.35 (13439) covalent geometry : angle 0.73349 / 0.39 (18372) hydrogen bonds : bond 0.04674 / 3.17 ( 641) hydrogen bonds : angle 4.47388 / 3.11 ( 1807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 125 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8217 (m-30) REVERT: B 36 TYR cc_start: 0.9078 (m-80) cc_final: 0.8766 (m-80) REVERT: B 44 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8712 (pt) REVERT: B 149 MET cc_start: 0.9304 (mmm) cc_final: 0.8978 (mmm) REVERT: B 213 TYR cc_start: 0.8707 (m-80) cc_final: 0.8333 (m-80) REVERT: B 216 TYR cc_start: 0.9228 (t80) cc_final: 0.8787 (t80) REVERT: D 96 MET cc_start: 0.9117 (tpp) cc_final: 0.8794 (tpp) REVERT: D 150 GLU cc_start: 0.9037 (tt0) cc_final: 0.8819 (tt0) REVERT: D 196 GLU cc_start: 0.7413 (tt0) cc_final: 0.6945 (mt-10) REVERT: I 135 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8353 (pmm) REVERT: I 242 ARG cc_start: 0.9165 (tpm170) cc_final: 0.8936 (tpm170) REVERT: I 259 MET cc_start: 0.8437 (pmm) cc_final: 0.7492 (pmm) REVERT: J 190 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8236 (mm-30) REVERT: J 253 MET cc_start: 0.8583 (tpp) cc_final: 0.8382 (tpp) REVERT: J 276 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8728 (tp) outliers start: 68 outliers final: 48 residues processed: 181 average time/residue: 0.0955 time to fit residues: 26.5711 Evaluate side-chains 171 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 119 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 140 ARG Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 259 MET Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 33 optimal weight: 5.9990 chunk 114 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN B 168 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS J 9 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.061540 restraints weight = 44268.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.063257 restraints weight = 24519.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.064479 restraints weight = 16722.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.065271 restraints weight = 12841.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.065881 restraints weight = 10752.744| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13439 Z= 0.152 Angle : 0.613 8.143 18372 Z= 0.327 Chirality : 0.042 0.162 2120 Planarity : 0.003 0.034 2160 Dihedral : 18.441 88.195 2197 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.37 % Favored : 95.49 % Rotamer: Outliers : 4.19 % Allowed : 30.82 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.20 (0.22), residues: 1465 helix: 1.35 (0.20), residues: 687 sheet: -1.40 (0.48), residues: 137 loop : -1.50 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 102 TYR 0.024 0.002 TYR A 216 PHE 0.024 0.001 PHE A 204 TRP 0.025 0.002 TRP I 3 HIS 0.008 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (13439) covalent geometry : angle 0.61311 / 0.33 (18372) hydrogen bonds : bond 0.03904 / 2.63 ( 641) hydrogen bonds : angle 4.13031 / 2.86 ( 1807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.9165 (tpp) cc_final: 0.8803 (tpp) REVERT: A 137 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8238 (tt) REVERT: B 36 TYR cc_start: 0.9024 (m-80) cc_final: 0.8681 (m-80) REVERT: B 44 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8675 (pt) REVERT: B 149 MET cc_start: 0.9259 (mmm) cc_final: 0.8912 (mmm) REVERT: B 213 TYR cc_start: 0.8631 (m-80) cc_final: 0.8281 (m-80) REVERT: B 216 TYR cc_start: 0.9199 (t80) cc_final: 0.8783 (t80) REVERT: D 96 MET cc_start: 0.9083 (tpp) cc_final: 0.8717 (tpp) REVERT: D 196 GLU cc_start: 0.7279 (tt0) cc_final: 0.6919 (mt-10) REVERT: I 135 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8216 (pmm) REVERT: I 242 ARG cc_start: 0.9215 (tpm170) cc_final: 0.8986 (tpm170) REVERT: I 259 MET cc_start: 0.8466 (pmm) cc_final: 0.7471 (pmm) REVERT: J 190 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8208 (mm-30) REVERT: J 276 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8634 (tp) outliers start: 56 outliers final: 43 residues processed: 186 average time/residue: 0.0859 time to fit residues: 24.4699 Evaluate side-chains 179 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 140 ARG Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 259 MET Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 89 HIS Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN J 19 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.083798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.053850 restraints weight = 44748.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.055701 restraints weight = 23436.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.056925 restraints weight = 15431.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.057756 restraints weight = 11700.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.058304 restraints weight = 9696.832| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13439 Z= 0.125 Angle : 0.615 10.306 18372 Z= 0.325 Chirality : 0.041 0.164 2120 Planarity : 0.003 0.035 2160 Dihedral : 18.299 89.012 2194 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.44 % Favored : 95.43 % Rotamer: Outliers : 3.44 % Allowed : 31.71 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.04 (0.22), residues: 1465 helix: 1.53 (0.20), residues: 679 sheet: -1.13 (0.47), residues: 143 loop : -1.37 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 102 TYR 0.020 0.001 TYR A 216 PHE 0.024 0.001 PHE A 204 TRP 0.023 0.002 TRP J 105 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (13439) covalent geometry : angle 0.61526 / 0.32 (18372) hydrogen bonds : bond 0.03707 / 2.49 ( 641) hydrogen bonds : angle 4.00766 / 2.76 ( 1807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.9140 (tpp) cc_final: 0.8772 (tpp) REVERT: A 110 TYR cc_start: 0.8842 (t80) cc_final: 0.8472 (t80) REVERT: A 164 LEU cc_start: 0.8859 (tp) cc_final: 0.8583 (mp) REVERT: B 36 TYR cc_start: 0.9001 (m-80) cc_final: 0.8602 (m-80) REVERT: B 44 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8557 (pt) REVERT: B 149 MET cc_start: 0.9278 (mmm) cc_final: 0.8941 (mmm) REVERT: B 213 TYR cc_start: 0.8628 (m-80) cc_final: 0.8288 (m-80) REVERT: B 216 TYR cc_start: 0.9195 (t80) cc_final: 0.8788 (t80) REVERT: D 96 MET cc_start: 0.9038 (tpp) cc_final: 0.8667 (tpp) REVERT: D 196 GLU cc_start: 0.7206 (tt0) cc_final: 0.6903 (mt-10) REVERT: I 135 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8150 (pmm) REVERT: I 242 ARG cc_start: 0.9240 (tpm170) cc_final: 0.9010 (tpm170) REVERT: I 259 MET cc_start: 0.8432 (pmm) cc_final: 0.7437 (pmm) REVERT: J 190 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8245 (mm-30) REVERT: J 249 MET cc_start: 0.8748 (mmm) cc_final: 0.8487 (mmm) REVERT: J 251 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8644 (t) REVERT: J 276 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8570 (tp) outliers start: 46 outliers final: 36 residues processed: 176 average time/residue: 0.0956 time to fit residues: 25.6437 Evaluate side-chains 176 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 140 ARG Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 124 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 0.1980 chunk 144 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN C 30 HIS J 9 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.094015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.063644 restraints weight = 44929.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.065399 restraints weight = 25241.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.066511 restraints weight = 17408.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.067348 restraints weight = 13670.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.067966 restraints weight = 11446.296| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13439 Z= 0.189 Angle : 0.634 9.730 18372 Z= 0.337 Chirality : 0.042 0.186 2120 Planarity : 0.003 0.037 2160 Dihedral : 18.281 88.508 2194 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.30 % Favored : 95.56 % Rotamer: Outliers : 3.44 % Allowed : 31.49 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.03 (0.22), residues: 1465 helix: 1.52 (0.20), residues: 679 sheet: -1.41 (0.46), residues: 147 loop : -1.39 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 4 TYR 0.020 0.002 TYR A 216 PHE 0.024 0.001 PHE A 204 TRP 0.065 0.004 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (13439) covalent geometry : angle 0.63387 / 0.34 (18372) hydrogen bonds : bond 0.03884 / 2.63 ( 641) hydrogen bonds : angle 4.09681 / 2.83 ( 1807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2930 Ramachandran restraints generated. 1465 Oldfield, 0 Emsley, 1465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.9176 (tpp) cc_final: 0.8815 (tpp) REVERT: B 36 TYR cc_start: 0.9029 (m-80) cc_final: 0.8636 (m-80) REVERT: B 44 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8645 (pt) REVERT: B 149 MET cc_start: 0.9301 (mmm) cc_final: 0.8983 (mmm) REVERT: B 213 TYR cc_start: 0.8626 (m-80) cc_final: 0.8260 (m-80) REVERT: B 216 TYR cc_start: 0.9209 (t80) cc_final: 0.8795 (t80) REVERT: D 96 MET cc_start: 0.9082 (tpp) cc_final: 0.8763 (tpp) REVERT: D 196 GLU cc_start: 0.7292 (tt0) cc_final: 0.6954 (mt-10) REVERT: I 135 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8197 (pmm) REVERT: I 153 ARG cc_start: 0.8108 (tpm170) cc_final: 0.7638 (tpm170) REVERT: I 242 ARG cc_start: 0.9232 (tpm170) cc_final: 0.9010 (tpm170) REVERT: I 259 MET cc_start: 0.8514 (pmm) cc_final: 0.7508 (pmm) REVERT: J 190 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8215 (tp30) REVERT: J 249 MET cc_start: 0.8698 (mmm) cc_final: 0.8439 (mmm) REVERT: J 253 MET cc_start: 0.8570 (tpp) cc_final: 0.8253 (tpp) REVERT: J 276 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8593 (tp) outliers start: 46 outliers final: 41 residues processed: 168 average time/residue: 0.0919 time to fit residues: 23.6427 Evaluate side-chains 171 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 140 ARG Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 276 LEU Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 93 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 142 optimal weight: 50.0000 chunk 62 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 ASN J 9 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.082666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.052526 restraints weight = 45094.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.054224 restraints weight = 25003.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.055373 restraints weight = 17050.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.056091 restraints weight = 13176.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.056623 restraints weight = 11116.150| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13439 Z= 0.183 Angle : 0.635 9.643 18372 Z= 0.337 Chirality : 0.042 0.172 2120 Planarity : 0.003 0.035 2160 Dihedral : 18.276 87.967 2194 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.30 % Favored : 95.56 % Rotamer: Outliers : 3.81 % Allowed : 31.11 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.05 (0.22), residues: 1465 helix: 1.51 (0.20), residues: 679 sheet: -1.44 (0.46), residues: 147 loop : -1.41 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 83 TYR 0.019 0.002 TYR A 216 PHE 0.024 0.001 PHE A 204 TRP 0.052 0.003 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (13439) covalent geometry : angle 0.63489 / 0.34 (18372) hydrogen bonds : bond 0.03834 / 2.60 ( 641) hydrogen bonds : angle 4.08867 / 2.82 ( 1807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1938.94 seconds wall clock time: 34 minutes 26.51 seconds (2066.51 seconds total)