Starting phenix.real_space_refine on Sun May 3 12:41:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vjb_65109/05_2026/9vjb_65109.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vjb_65109/05_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_65109/05_2026/9vjb_65109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vjb_65109/05_2026/9vjb_65109.map" model { file = "/net/cci-nas-00/data/ceres_data/9vjb_65109/05_2026/9vjb_65109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vjb_65109/05_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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: 3.24, per 1000 atoms: 0.25 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: 0.89 Conformation dependent library (CDL) restraints added in 534.4 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: 1.49 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: 2.17 Time building geometry restraints manager: 1.22 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=" 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 bond pdb=" N MET J 259 " pdb=" CA MET J 259 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.27e-02 6.20e+03 6.26e+00 bond pdb=" N LEU J 261 " pdb=" CA LEU J 261 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.12e+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: 1954 0.097 - 0.194: 152 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.400 Find NCS groups from input model: 0.250 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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= 0.243 Angle : 1.018 17.959 18372 Z= 0.542 Chirality : 0.054 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 covalent geometry : bond 0.00471 (13439) covalent geometry : angle 1.01771 (18372) hydrogen bonds : bond 0.15082 ( 641) hydrogen bonds : angle 6.02957 ( 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 : 0.503 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: 0.1125 time to fit residues: 59.1001 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 : 0.519 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 168 ASN A 202 ASN B 115 HIS B 168 ASN B 189 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN D 106 GLN D 153 GLN D 188 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 HIS J 258 GLN J 277 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.092923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.062643 restraints weight = 44281.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.064426 restraints weight = 24312.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065683 restraints weight = 16480.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.066568 restraints weight = 12538.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067092 restraints weight = 10432.886| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13439 Z= 0.226 Angle : 0.676 7.933 18372 Z= 0.362 Chirality : 0.043 0.230 2120 Planarity : 0.005 0.069 2160 Dihedral : 18.342 84.709 2221 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.16 % Favored : 95.56 % Rotamer: Outliers : 6.21 % Allowed : 29.17 % Favored : 64.62 % 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: -0.77 (0.21), residues: 1465 helix: 0.61 (0.19), residues: 686 sheet: -0.92 (0.47), residues: 141 loop : -1.66 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 102 TYR 0.023 0.002 TYR A 206 PHE 0.033 0.002 PHE D 145 TRP 0.029 0.002 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00508 (13439) covalent geometry : angle 0.67629 (18372) hydrogen bonds : bond 0.04322 ( 641) hydrogen bonds : angle 4.33378 ( 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 242 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 159 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.9127 (tpp) cc_final: 0.8917 (tpp) REVERT: A 138 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.5406 (pt0) REVERT: A 142 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8564 (m-30) REVERT: B 44 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8704 (pt) REVERT: B 213 TYR cc_start: 0.8623 (m-80) cc_final: 0.8379 (m-80) REVERT: B 216 TYR cc_start: 0.9195 (t80) cc_final: 0.8742 (t80) REVERT: D 50 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8359 (tp-100) REVERT: D 96 MET cc_start: 0.9151 (tpp) cc_final: 0.8719 (tpp) REVERT: D 150 GLU cc_start: 0.9009 (tt0) cc_final: 0.8770 (tt0) REVERT: D 196 GLU cc_start: 0.7319 (tt0) cc_final: 0.7001 (mt-10) REVERT: I 249 MET cc_start: 0.8918 (ptp) cc_final: 0.8698 (ptp) REVERT: J 166 ARG cc_start: 0.8453 (mmm160) cc_final: 0.8231 (tpp-160) REVERT: J 190 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8911 (mm-30) outliers start: 83 outliers final: 36 residues processed: 232 average time/residue: 0.1039 time to fit residues: 36.2644 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 : 0.436 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain A residue 138 GLU 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 182 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 59 LEU 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 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 D residue 170 CYS Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain I residue 7 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 I residue 200 LEU Chi-restraints excluded: chain J residue 47 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 192 VAL Chi-restraints excluded: chain J residue 198 THR 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: 8.9990 chunk 73 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 53 optimal weight: 0.0980 chunk 103 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN A 201 GLN B 168 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.093209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.062886 restraints weight = 45019.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.064693 restraints weight = 24478.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.065974 restraints weight = 16530.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.066770 restraints weight = 12589.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067150 restraints weight = 10542.462| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13439 Z= 0.163 Angle : 0.606 7.585 18372 Z= 0.324 Chirality : 0.041 0.221 2120 Planarity : 0.003 0.049 2160 Dihedral : 18.243 86.047 2203 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.89 % Favored : 95.90 % Rotamer: Outliers : 4.56 % Allowed : 29.84 % Favored : 65.59 % 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: -0.20 (0.22), residues: 1465 helix: 1.19 (0.20), residues: 684 sheet: -0.94 (0.42), residues: 169 loop : -1.41 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 203 TYR 0.018 0.001 TYR J 155 PHE 0.018 0.001 PHE D 145 TRP 0.028 0.002 TRP I 3 HIS 0.014 0.001 HIS J 119 Details of bonding type rmsd covalent geometry : bond 0.00369 (13439) covalent geometry : angle 0.60594 (18372) hydrogen bonds : bond 0.03867 ( 641) hydrogen bonds : angle 4.11679 ( 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 203 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 142 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8638 (pptt) REVERT: A 88 ASN cc_start: 0.9220 (t0) cc_final: 0.8999 (m-40) REVERT: A 96 MET cc_start: 0.9162 (tpp) cc_final: 0.8931 (tpp) REVERT: A 142 ASP cc_start: 0.9147 (OUTLIER) cc_final: 0.8177 (m-30) REVERT: A 206 TYR cc_start: 0.7222 (m-80) cc_final: 0.6922 (m-10) REVERT: B 36 TYR cc_start: 0.8884 (m-80) cc_final: 0.8662 (m-80) REVERT: B 44 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8636 (pt) REVERT: B 213 TYR cc_start: 0.8567 (m-80) cc_final: 0.8319 (m-10) REVERT: B 216 TYR cc_start: 0.9219 (t80) cc_final: 0.8774 (t80) REVERT: D 50 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8494 (tp-100) REVERT: D 96 MET cc_start: 0.9123 (tpp) cc_final: 0.8689 (tpp) REVERT: D 150 GLU cc_start: 0.8976 (tt0) cc_final: 0.8768 (tt0) REVERT: D 196 GLU cc_start: 0.7170 (tt0) cc_final: 0.6879 (mt-10) REVERT: I 135 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8232 (pmm) REVERT: I 249 MET cc_start: 0.8931 (ptp) cc_final: 0.8716 (ptp) REVERT: J 190 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8026 (tp30) REVERT: J 251 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8582 (t) outliers start: 61 outliers final: 36 residues processed: 190 average time/residue: 0.0941 time to fit residues: 27.6773 Evaluate side-chains 172 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 70 VAL 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 125 THR 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 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 214 LEU Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain I residue 6 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 47 ILE Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 93 GLN Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 259 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 57 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 134 optimal weight: 0.0370 chunk 100 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN B 168 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 157 ASN J 29 GLN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 HIS ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.092656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.062350 restraints weight = 44688.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.064177 restraints weight = 24163.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065418 restraints weight = 16207.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.066220 restraints weight = 12360.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.066768 restraints weight = 10330.971| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13439 Z= 0.142 Angle : 0.575 8.031 18372 Z= 0.307 Chirality : 0.040 0.193 2120 Planarity : 0.003 0.042 2160 Dihedral : 18.092 85.844 2199 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.96 % Favored : 95.84 % Rotamer: Outliers : 4.41 % Allowed : 29.09 % Favored : 66.49 % 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: 0.09 (0.22), residues: 1465 helix: 1.48 (0.20), residues: 678 sheet: -0.86 (0.43), residues: 169 loop : -1.30 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 222 TYR 0.015 0.001 TYR A 216 PHE 0.021 0.001 PHE A 204 TRP 0.033 0.002 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00320 (13439) covalent geometry : angle 0.57494 (18372) hydrogen bonds : bond 0.03623 ( 641) hydrogen bonds : angle 3.94831 ( 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 202 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 143 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9128 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: A 206 TYR cc_start: 0.7320 (m-80) cc_final: 0.7049 (m-80) REVERT: A 211 ASN cc_start: 0.9143 (m-40) cc_final: 0.8757 (m-40) REVERT: B 36 TYR cc_start: 0.8878 (m-80) cc_final: 0.8494 (m-80) REVERT: B 44 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8615 (pt) REVERT: B 149 MET cc_start: 0.9337 (mmm) cc_final: 0.9066 (mmm) REVERT: B 213 TYR cc_start: 0.8546 (m-80) cc_final: 0.8286 (m-80) REVERT: B 216 TYR cc_start: 0.9213 (t80) cc_final: 0.8751 (t80) REVERT: D 96 MET cc_start: 0.9158 (tpp) cc_final: 0.8732 (tpp) REVERT: D 110 TYR cc_start: 0.9182 (m-10) cc_final: 0.8970 (m-80) REVERT: D 196 GLU cc_start: 0.7192 (tt0) cc_final: 0.6954 (mt-10) REVERT: I 135 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8215 (pmm) REVERT: I 190 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7946 (tp30) REVERT: I 259 MET cc_start: 0.8525 (pmm) cc_final: 0.7479 (pmm) REVERT: J 140 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7142 (ptt-90) REVERT: J 190 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8025 (tp30) REVERT: J 251 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8631 (t) REVERT: J 276 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8639 (tp) outliers start: 59 outliers final: 36 residues processed: 190 average time/residue: 0.1004 time to fit residues: 29.4326 Evaluate side-chains 178 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 124 ILE 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 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 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 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 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 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 190 GLU Chi-restraints excluded: chain J residue 211 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 56 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 GLN J 9 ASN J 227 GLN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.091434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.061168 restraints weight = 44960.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.062926 restraints weight = 24714.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.064109 restraints weight = 16800.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.064936 restraints weight = 12923.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.065460 restraints weight = 10809.033| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13439 Z= 0.196 Angle : 0.604 7.265 18372 Z= 0.323 Chirality : 0.041 0.181 2120 Planarity : 0.003 0.037 2160 Dihedral : 18.111 84.099 2196 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.44 % Favored : 95.43 % Rotamer: Outliers : 4.94 % Allowed : 29.17 % Favored : 65.89 % 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: 0.10 (0.22), residues: 1465 helix: 1.52 (0.20), residues: 679 sheet: -1.07 (0.47), residues: 147 loop : -1.28 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 242 TYR 0.017 0.002 TYR A 216 PHE 0.017 0.001 PHE A 204 TRP 0.038 0.003 TRP I 3 HIS 0.008 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00444 (13439) covalent geometry : angle 0.60355 (18372) hydrogen bonds : bond 0.03866 ( 641) hydrogen bonds : angle 4.07385 ( 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: 66 poor density : 133 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.9269 (OUTLIER) cc_final: 0.8547 (m-30) REVERT: A 206 TYR cc_start: 0.7450 (m-80) cc_final: 0.7082 (m-80) REVERT: B 44 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8662 (pt) REVERT: B 149 MET cc_start: 0.9324 (mmm) cc_final: 0.8982 (mmm) REVERT: B 213 TYR cc_start: 0.8607 (m-80) cc_final: 0.8268 (m-10) REVERT: D 96 MET cc_start: 0.9171 (tpp) cc_final: 0.8745 (tpp) REVERT: D 110 TYR cc_start: 0.9216 (m-10) cc_final: 0.9015 (m-80) REVERT: D 117 MET cc_start: 0.8687 (mmp) cc_final: 0.8444 (mmp) REVERT: D 196 GLU cc_start: 0.7265 (tt0) cc_final: 0.6856 (mt-10) REVERT: I 135 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8222 (pmm) REVERT: I 259 MET cc_start: 0.8417 (pmm) cc_final: 0.7556 (pmm) REVERT: J 41 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8869 (tt) REVERT: J 190 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8037 (tp30) REVERT: J 251 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8668 (t) REVERT: J 276 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8534 (tp) outliers start: 66 outliers final: 46 residues processed: 185 average time/residue: 0.0975 time to fit residues: 27.8878 Evaluate side-chains 172 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 119 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain A residue 59 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 158 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 1 MET 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 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 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 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 142 ASP Chi-restraints excluded: chain C residue 214 LEU 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 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 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 190 GLU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 211 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 113 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 141 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 133 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.084298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.054795 restraints weight = 45305.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.056675 restraints weight = 23682.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.057908 restraints weight = 15618.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.058602 restraints weight = 11847.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059230 restraints weight = 10013.992| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13439 Z= 0.110 Angle : 0.560 8.701 18372 Z= 0.297 Chirality : 0.039 0.161 2120 Planarity : 0.003 0.038 2160 Dihedral : 17.976 85.268 2196 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.75 % Favored : 96.11 % Rotamer: Outliers : 3.22 % Allowed : 31.79 % Favored : 65.00 % 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: 0.42 (0.23), residues: 1465 helix: 1.72 (0.20), residues: 682 sheet: -0.52 (0.44), residues: 169 loop : -1.16 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 4 TYR 0.013 0.001 TYR A 184 PHE 0.020 0.001 PHE A 204 TRP 0.040 0.003 TRP I 3 HIS 0.008 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00237 (13439) covalent geometry : angle 0.56041 (18372) hydrogen bonds : bond 0.03280 ( 641) hydrogen bonds : angle 3.76513 ( 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 191 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 110 TYR cc_start: 0.8807 (t80) cc_final: 0.8532 (t80) REVERT: A 164 LEU cc_start: 0.8814 (tp) cc_final: 0.8492 (mp) REVERT: A 202 ASN cc_start: 0.9124 (m-40) cc_final: 0.8915 (m110) REVERT: A 213 TYR cc_start: 0.8552 (m-80) cc_final: 0.8218 (m-80) REVERT: A 216 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7800 (t80) REVERT: B 1 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7741 (mmp) REVERT: B 213 TYR cc_start: 0.8552 (m-80) cc_final: 0.8261 (m-80) REVERT: D 96 MET cc_start: 0.9125 (tpp) cc_final: 0.8682 (tpp) REVERT: D 131 LYS cc_start: 0.9572 (tppp) cc_final: 0.9353 (ttmm) REVERT: I 135 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8173 (pmm) REVERT: I 153 ARG cc_start: 0.7978 (tpm170) cc_final: 0.7596 (tpm170) REVERT: I 259 MET cc_start: 0.8559 (pmm) cc_final: 0.7772 (pmm) REVERT: J 190 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.7947 (tp30) REVERT: J 240 MET cc_start: 0.9088 (mtm) cc_final: 0.8600 (mtp) REVERT: J 251 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8777 (t) REVERT: J 276 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8458 (tp) outliers start: 43 outliers final: 31 residues processed: 183 average time/residue: 0.0984 time to fit residues: 28.0186 Evaluate side-chains 171 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE 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 57 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 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 1 MET Chi-restraints excluded: chain B residue 25 VAL 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 C residue 25 VAL Chi-restraints excluded: chain C residue 42 ASN 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 118 ASP Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 173 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 140 ARG Chi-restraints excluded: chain J residue 190 GLU Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 251 THR Chi-restraints excluded: chain J residue 276 LEU 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: 8.9990 chunk 103 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN J 115 ASN J 193 GLN ** 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 = 0.3484 r_free = 0.3484 target = 0.078004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.048105 restraints weight = 46546.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.049744 restraints weight = 25518.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.050760 restraints weight = 17342.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.051484 restraints weight = 13523.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.051900 restraints weight = 11402.704| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 13439 Z= 0.391 Angle : 0.782 8.071 18372 Z= 0.411 Chirality : 0.045 0.196 2120 Planarity : 0.004 0.034 2160 Dihedral : 18.424 81.376 2194 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.48 % Favored : 93.38 % Rotamer: Outliers : 5.39 % Allowed : 30.07 % Favored : 64.55 % 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: -0.27 (0.22), residues: 1465 helix: 1.16 (0.19), residues: 680 sheet: -0.95 (0.45), residues: 163 loop : -1.48 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 4 TYR 0.024 0.002 TYR A 216 PHE 0.022 0.002 PHE B 28 TRP 0.047 0.004 TRP I 3 HIS 0.008 0.002 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00875 (13439) covalent geometry : angle 0.78228 (18372) hydrogen bonds : bond 0.04992 ( 641) hydrogen bonds : angle 4.61723 ( 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 195 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 123 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 CYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8764 (t) REVERT: A 211 ASN cc_start: 0.9086 (m-40) cc_final: 0.8742 (m110) REVERT: A 213 TYR cc_start: 0.8587 (m-80) cc_final: 0.8306 (m-80) REVERT: B 44 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8770 (pt) REVERT: B 213 TYR cc_start: 0.8633 (m-80) cc_final: 0.8315 (m-80) REVERT: D 96 MET cc_start: 0.9155 (tpp) cc_final: 0.8803 (tpp) REVERT: D 110 TYR cc_start: 0.9349 (m-80) cc_final: 0.9112 (m-80) REVERT: I 135 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8388 (pmm) REVERT: I 259 MET cc_start: 0.8268 (pmm) cc_final: 0.7548 (pmm) REVERT: J 41 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8919 (tt) REVERT: J 190 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8228 (tp30) REVERT: J 276 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8670 (tp) outliers start: 72 outliers final: 47 residues processed: 180 average time/residue: 0.0952 time to fit residues: 26.5691 Evaluate side-chains 166 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 113 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 158 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 B residue 1 MET 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 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 142 ASP Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 62 VAL 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 I residue 191 LEU Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 41 LEU 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 183 LEU Chi-restraints excluded: chain J residue 190 GLU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 276 LEU 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: 0.7980 chunk 114 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 0.0670 chunk 57 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 168 ASN J 9 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.083847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.053892 restraints weight = 44896.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.055661 restraints weight = 24407.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.056796 restraints weight = 16500.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.057589 restraints weight = 12791.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.057999 restraints weight = 10755.326| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13439 Z= 0.120 Angle : 0.604 9.458 18372 Z= 0.319 Chirality : 0.041 0.164 2120 Planarity : 0.003 0.036 2160 Dihedral : 18.160 82.967 2194 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.82 % Favored : 96.04 % Rotamer: Outliers : 2.69 % Allowed : 32.83 % Favored : 64.47 % 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: 0.25 (0.23), residues: 1465 helix: 1.61 (0.20), residues: 682 sheet: -0.78 (0.42), residues: 179 loop : -1.23 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 4 TYR 0.020 0.001 TYR A 206 PHE 0.024 0.001 PHE A 204 TRP 0.051 0.003 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00264 (13439) covalent geometry : angle 0.60372 (18372) hydrogen bonds : bond 0.03447 ( 641) hydrogen bonds : angle 3.91444 ( 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 169 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.8884 (tp) cc_final: 0.8469 (mp) REVERT: A 170 CYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8479 (t) REVERT: A 202 ASN cc_start: 0.9257 (m-40) cc_final: 0.9053 (m110) REVERT: A 206 TYR cc_start: 0.6855 (m-80) cc_final: 0.6453 (m-80) REVERT: A 213 TYR cc_start: 0.8533 (m-80) cc_final: 0.8235 (m-80) REVERT: B 44 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8585 (pt) REVERT: B 149 MET cc_start: 0.9149 (mmm) cc_final: 0.8907 (mmm) REVERT: D 96 MET cc_start: 0.9098 (tpp) cc_final: 0.8678 (tpp) REVERT: D 131 LYS cc_start: 0.9572 (tppp) cc_final: 0.9347 (ttmm) REVERT: I 135 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8295 (pmm) REVERT: I 259 MET cc_start: 0.8453 (pmm) cc_final: 0.7736 (pmm) REVERT: J 41 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8852 (tt) REVERT: J 190 GLU cc_start: 0.9006 (mm-30) cc_final: 0.7986 (tp30) REVERT: J 251 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8825 (t) REVERT: J 276 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8507 (tp) outliers start: 36 outliers final: 24 residues processed: 163 average time/residue: 0.1048 time to fit residues: 25.9909 Evaluate side-chains 153 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 42 ASN 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 D residue 62 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain I residue 257 LYS Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 47 ILE 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 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 137 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.082628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.052688 restraints weight = 45512.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.054418 restraints weight = 25069.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.055563 restraints weight = 17024.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.056324 restraints weight = 13170.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.056723 restraints weight = 11091.629| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4777 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= 0.152 Angle : 0.609 9.756 18372 Z= 0.321 Chirality : 0.040 0.168 2120 Planarity : 0.003 0.034 2160 Dihedral : 18.148 81.575 2194 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.10 % Favored : 95.77 % Rotamer: Outliers : 3.14 % Allowed : 32.91 % Favored : 63.95 % 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: 0.30 (0.23), residues: 1465 helix: 1.65 (0.20), residues: 682 sheet: -0.74 (0.43), residues: 169 loop : -1.20 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 222 TYR 0.020 0.001 TYR A 206 PHE 0.023 0.001 PHE A 212 TRP 0.050 0.003 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00350 (13439) covalent geometry : angle 0.60946 (18372) hydrogen bonds : bond 0.03606 ( 641) hydrogen bonds : angle 3.90403 ( 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 166 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.9062 (tpp) cc_final: 0.8834 (tpp) REVERT: A 164 LEU cc_start: 0.8893 (tp) cc_final: 0.8557 (mp) REVERT: A 170 CYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8532 (t) REVERT: A 202 ASN cc_start: 0.9274 (m-40) cc_final: 0.9014 (m110) REVERT: A 211 ASN cc_start: 0.9104 (m-40) cc_final: 0.8630 (m110) REVERT: A 213 TYR cc_start: 0.8512 (m-80) cc_final: 0.8265 (m-80) REVERT: B 44 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8614 (pt) REVERT: B 149 MET cc_start: 0.9236 (mmm) cc_final: 0.8971 (mmm) REVERT: D 96 MET cc_start: 0.9122 (tpp) cc_final: 0.8708 (tpp) REVERT: I 135 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8326 (pmm) REVERT: I 259 MET cc_start: 0.8351 (pmm) cc_final: 0.7656 (pmm) REVERT: J 41 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8890 (tt) REVERT: J 190 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8114 (mm-30) REVERT: J 240 MET cc_start: 0.9065 (mtm) cc_final: 0.8858 (mtp) REVERT: J 251 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8744 (t) REVERT: J 276 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8613 (tp) outliers start: 42 outliers final: 30 residues processed: 159 average time/residue: 0.0972 time to fit residues: 24.0853 Evaluate side-chains 154 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 170 CYS 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 125 THR 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 D residue 62 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 135 MET Chi-restraints excluded: chain I residue 257 LYS Chi-restraints excluded: chain J residue 41 LEU 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 211 PHE 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 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 124 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 144 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.083594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.053765 restraints weight = 45746.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.055521 restraints weight = 25018.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.056640 restraints weight = 16938.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.057438 restraints weight = 13140.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.057838 restraints weight = 11064.877| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13439 Z= 0.126 Angle : 0.612 10.277 18372 Z= 0.321 Chirality : 0.040 0.170 2120 Planarity : 0.003 0.034 2160 Dihedral : 18.043 82.035 2194 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.89 % Favored : 95.97 % Rotamer: Outliers : 3.07 % Allowed : 32.98 % Favored : 63.95 % 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: 0.34 (0.23), residues: 1465 helix: 1.71 (0.20), residues: 684 sheet: -0.78 (0.42), residues: 179 loop : -1.21 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 222 TYR 0.025 0.001 TYR D 110 PHE 0.029 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 covalent geometry : bond 0.00283 (13439) covalent geometry : angle 0.61167 (18372) hydrogen bonds : bond 0.03406 ( 641) hydrogen bonds : angle 3.79890 ( 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 170 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.9075 (tpp) cc_final: 0.8841 (tpp) REVERT: A 164 LEU cc_start: 0.8795 (tp) cc_final: 0.8404 (mp) REVERT: A 170 CYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8501 (t) REVERT: A 196 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7337 (mm-30) REVERT: A 202 ASN cc_start: 0.9219 (m-40) cc_final: 0.8990 (m-40) REVERT: A 213 TYR cc_start: 0.8597 (m-80) cc_final: 0.8251 (m-80) REVERT: B 44 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8603 (pt) REVERT: B 149 MET cc_start: 0.9231 (mmm) cc_final: 0.8949 (mmm) REVERT: D 96 MET cc_start: 0.9106 (tpp) cc_final: 0.8680 (tpp) REVERT: I 153 ARG cc_start: 0.8056 (tpm170) cc_final: 0.7594 (tpm170) REVERT: I 259 MET cc_start: 0.8432 (pmm) cc_final: 0.7762 (pmm) REVERT: J 41 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8872 (tt) REVERT: J 190 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8121 (mm-30) REVERT: J 240 MET cc_start: 0.8976 (mtm) cc_final: 0.8701 (mtp) REVERT: J 251 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8692 (t) REVERT: J 276 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8597 (tp) outliers start: 41 outliers final: 32 residues processed: 163 average time/residue: 0.0966 time to fit residues: 24.4646 Evaluate side-chains 167 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 196 GLU 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 125 THR 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 149 MET Chi-restraints excluded: chain D residue 62 VAL 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 I residue 257 LYS Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 140 ARG Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 211 PHE 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 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 93 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 142 optimal weight: 30.0000 chunk 62 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 ASN J 115 ASN ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.082177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.052033 restraints weight = 45258.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.053686 restraints weight = 25590.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.054786 restraints weight = 17659.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.055508 restraints weight = 13867.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.055989 restraints weight = 11759.988| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13439 Z= 0.230 Angle : 0.665 10.418 18372 Z= 0.348 Chirality : 0.041 0.176 2120 Planarity : 0.003 0.033 2160 Dihedral : 18.133 83.000 2194 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.85 % Favored : 95.02 % Rotamer: Outliers : 3.29 % Allowed : 32.98 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1465 helix: 1.60 (0.20), residues: 684 sheet: -0.81 (0.43), residues: 169 loop : -1.24 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 222 TYR 0.019 0.002 TYR J 180 PHE 0.023 0.002 PHE A 204 TRP 0.055 0.004 TRP I 3 HIS 0.009 0.001 HIS I 150 Details of bonding type rmsd covalent geometry : bond 0.00525 (13439) covalent geometry : angle 0.66469 (18372) hydrogen bonds : bond 0.03954 ( 641) hydrogen bonds : angle 4.06802 ( 1807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2173.24 seconds wall clock time: 38 minutes 32.20 seconds (2312.20 seconds total)