Starting phenix.real_space_refine on Wed Feb 4 12:55:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9doq_47088/02_2026/9doq_47088.cif Found real_map, /net/cci-nas-00/data/ceres_data/9doq_47088/02_2026/9doq_47088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9doq_47088/02_2026/9doq_47088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9doq_47088/02_2026/9doq_47088.map" model { file = "/net/cci-nas-00/data/ceres_data/9doq_47088/02_2026/9doq_47088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9doq_47088/02_2026/9doq_47088.cif" } resolution = 3.26 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= 0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 39 5.16 5 C 6785 2.51 5 N 1805 2.21 5 O 1907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10540 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1841 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1841 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "G" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2763 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 15, 'TRANS': 338} Chain: "F" Number of atoms: 2838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2838 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 344} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1065 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 130} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 2.35, per 1000 atoms: 0.22 Number of scatterers: 10540 At special positions: 0 Unit cell: (69.12, 97.2, 164.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 4 15.00 O 1907 8.00 N 1805 7.00 C 6785 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: 0.57 Conformation dependent library (CDL) restraints added in 464.8 milliseconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 53.0% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 71 through 79 Processing helix chain 'B' and resid 94 through 104 removed outlier: 4.312A pdb=" N ILE B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 125 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 139 through 154 Processing helix chain 'B' and resid 169 through 187 removed outlier: 4.191A pdb=" N GLY B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 71 through 79 Processing helix chain 'A' and resid 94 through 106 removed outlier: 4.182A pdb=" N ILE A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 139 through 154 removed outlier: 3.781A pdb=" N SER A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 186 removed outlier: 4.040A pdb=" N GLY A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'G' and resid 2 through 36 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 44 through 82 Proline residue: G 57 - end of helix Proline residue: G 65 - end of helix removed outlier: 3.747A pdb=" N ASN G 82 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 91 Processing helix chain 'G' and resid 94 through 137 Proline residue: G 105 - end of helix Proline residue: G 122 - end of helix Processing helix chain 'G' and resid 230 through 238 removed outlier: 3.677A pdb=" N VAL G 238 " --> pdb=" O LEU G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 244 removed outlier: 3.792A pdb=" N LEU G 244 " --> pdb=" O PRO G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 259 removed outlier: 3.614A pdb=" N GLN G 259 " --> pdb=" O TYR G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 275 Processing helix chain 'G' and resid 275 through 293 Processing helix chain 'G' and resid 299 through 329 Proline residue: G 323 - end of helix removed outlier: 3.829A pdb=" N LEU G 326 " --> pdb=" O GLY G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 353 removed outlier: 3.999A pdb=" N ALA G 335 " --> pdb=" O PRO G 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL G 336 " --> pdb=" O PRO G 332 " (cutoff:3.500A) Proline residue: G 339 - end of helix Processing helix chain 'F' and resid 2 through 40 removed outlier: 3.770A pdb=" N LYS F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 47 through 82 Proline residue: F 57 - end of helix removed outlier: 3.785A pdb=" N LEU F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 83 through 90 Processing helix chain 'F' and resid 94 through 120 removed outlier: 4.093A pdb=" N ALA F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) Proline residue: F 105 - end of helix Processing helix chain 'F' and resid 120 through 133 Processing helix chain 'F' and resid 135 through 143 Processing helix chain 'F' and resid 249 through 254 removed outlier: 3.936A pdb=" N ALA F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL F 254 " --> pdb=" O GLU F 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 249 through 254' Processing helix chain 'F' and resid 255 through 260 removed outlier: 3.749A pdb=" N LEU F 259 " --> pdb=" O PRO F 255 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 260' Processing helix chain 'F' and resid 264 through 275 Processing helix chain 'F' and resid 275 through 289 removed outlier: 4.177A pdb=" N LEU F 279 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL F 289 " --> pdb=" O THR F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 293 removed outlier: 3.631A pdb=" N ARG F 293 " --> pdb=" O PRO F 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 290 through 293' Processing helix chain 'F' and resid 304 through 327 Processing helix chain 'F' and resid 336 through 352 removed outlier: 4.189A pdb=" N HIS F 340 " --> pdb=" O LEU F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 361 Processing helix chain 'C' and resid 113 through 117 removed outlier: 4.247A pdb=" N GLU C 116 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL C 117 " --> pdb=" O GLY C 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 113 through 117' Processing sheet with id=AA1, first strand: chain 'B' and resid 19 through 27 removed outlier: 6.618A pdb=" N ARG B 20 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B 10 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL B 22 " --> pdb=" O HIS B 8 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N HIS B 8 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU B 9 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN B 57 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 160 removed outlier: 6.964A pdb=" N ILE B 209 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 27 removed outlier: 6.313A pdb=" N VAL A 18 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER A 12 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG A 20 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA A 10 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 22 " --> pdb=" O HIS A 8 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 9 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN A 57 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 158 through 159 removed outlier: 3.580A pdb=" N ALA A 217 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 148 through 152 removed outlier: 7.148A pdb=" N GLY G 170 " --> pdb=" O ASN G 160 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL G 162 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU G 168 " --> pdb=" O VAL G 162 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL G 167 " --> pdb=" O ARG G 192 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG G 192 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR G 169 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG G 190 " --> pdb=" O TYR G 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 148 through 152 removed outlier: 7.148A pdb=" N GLY G 170 " --> pdb=" O ASN G 160 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL G 162 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU G 168 " --> pdb=" O VAL G 162 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL G 167 " --> pdb=" O ARG G 192 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG G 192 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR G 169 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG G 190 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA G 188 " --> pdb=" O VAL G 203 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL G 203 " --> pdb=" O ALA G 188 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG G 190 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU G 201 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP G 198 " --> pdb=" O TRP G 225 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP G 225 " --> pdb=" O TRP G 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 160 through 161 removed outlier: 3.875A pdb=" N GLY F 215 " --> pdb=" O TYR F 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 199 through 201 removed outlier: 3.544A pdb=" N VAL F 237 " --> pdb=" O LEU F 210 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR F 235 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET F 238 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ASP C 49 " --> pdb=" O MET F 238 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N HIS C 77 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR C 51 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU C 75 " --> pdb=" O TYR C 51 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU C 53 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL C 73 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA C 55 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR C 71 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER C 57 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU C 69 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN C 59 " --> pdb=" O ASP C 67 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR C 87 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C 75 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE C 85 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AB1, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB2, first strand: chain 'C' and resid 150 through 152 588 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1866 1.32 - 1.44: 2560 1.44 - 1.56: 6224 1.56 - 1.68: 8 1.68 - 1.80: 72 Bond restraints: 10730 Sorted by residual: bond pdb=" CA SER F 177 " pdb=" C SER F 177 " ideal model delta sigma weight residual 1.521 1.495 0.026 1.19e-02 7.06e+03 4.75e+00 bond pdb=" C ILE F 176 " pdb=" O ILE F 176 " ideal model delta sigma weight residual 1.237 1.223 0.014 1.09e-02 8.42e+03 1.61e+00 bond pdb=" CA ILE F 176 " pdb=" CB ILE F 176 " ideal model delta sigma weight residual 1.538 1.525 0.013 1.30e-02 5.92e+03 1.05e+00 bond pdb=" C PHE F 175 " pdb=" O PHE F 175 " ideal model delta sigma weight residual 1.235 1.224 0.011 1.12e-02 7.97e+03 9.92e-01 bond pdb=" CA PHE F 175 " pdb=" CB PHE F 175 " ideal model delta sigma weight residual 1.532 1.517 0.015 1.58e-02 4.01e+03 8.73e-01 ... (remaining 10725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 14232 1.17 - 2.34: 188 2.34 - 3.52: 66 3.52 - 4.69: 8 4.69 - 5.86: 2 Bond angle restraints: 14496 Sorted by residual: angle pdb=" N ILE F 176 " pdb=" CA ILE F 176 " pdb=" C ILE F 176 " ideal model delta sigma weight residual 107.77 111.17 -3.40 1.48e+00 4.57e-01 5.28e+00 angle pdb=" N SER F 184 " pdb=" CA SER F 184 " pdb=" CB SER F 184 " ideal model delta sigma weight residual 113.65 110.37 3.28 1.47e+00 4.63e-01 4.99e+00 angle pdb=" C ILE F 176 " pdb=" CA ILE F 176 " pdb=" CB ILE F 176 " ideal model delta sigma weight residual 110.42 107.46 2.96 1.35e+00 5.49e-01 4.81e+00 angle pdb=" CB MET C 70 " pdb=" CG MET C 70 " pdb=" SD MET C 70 " ideal model delta sigma weight residual 112.70 118.15 -5.45 3.00e+00 1.11e-01 3.30e+00 angle pdb=" CA TYR C 51 " pdb=" CB TYR C 51 " pdb=" CG TYR C 51 " ideal model delta sigma weight residual 113.90 117.09 -3.19 1.80e+00 3.09e-01 3.13e+00 ... (remaining 14491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.27: 5846 23.27 - 46.53: 566 46.53 - 69.80: 73 69.80 - 93.07: 13 93.07 - 116.33: 1 Dihedral angle restraints: 6499 sinusoidal: 2692 harmonic: 3807 Sorted by residual: dihedral pdb=" O21 3PE F 402 " pdb=" C2 3PE F 402 " pdb=" C3 3PE F 402 " pdb=" O31 3PE F 402 " ideal model delta sinusoidal sigma weight residual 60.47 176.80 -116.33 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" CA ASP B 162 " pdb=" CB ASP B 162 " pdb=" CG ASP B 162 " pdb=" OD1 ASP B 162 " ideal model delta sinusoidal sigma weight residual -30.00 -86.98 56.98 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CG ARG G 6 " pdb=" CD ARG G 6 " pdb=" NE ARG G 6 " pdb=" CZ ARG G 6 " ideal model delta sinusoidal sigma weight residual -90.00 -134.96 44.96 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 6496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1008 0.024 - 0.048: 366 0.048 - 0.072: 158 0.072 - 0.096: 60 0.096 - 0.121: 67 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CA VAL F 254 " pdb=" N VAL F 254 " pdb=" C VAL F 254 " pdb=" CB VAL F 254 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE C 48 " pdb=" N ILE C 48 " pdb=" C ILE C 48 " pdb=" CB ILE C 48 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA ILE C 103 " pdb=" N ILE C 103 " pdb=" C ILE C 103 " pdb=" CB ILE C 103 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 1656 not shown) Planarity restraints: 1833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 117 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C GLY G 117 " -0.037 2.00e-02 2.50e+03 pdb=" O GLY G 117 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU G 118 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 354 " -0.023 5.00e-02 4.00e+02 3.56e-02 2.02e+00 pdb=" N PRO F 355 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO F 355 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 355 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 277 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO F 278 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO F 278 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 278 " -0.019 5.00e-02 4.00e+02 ... (remaining 1830 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 78 2.58 - 3.16: 9101 3.16 - 3.74: 15485 3.74 - 4.32: 21338 4.32 - 4.90: 37216 Nonbonded interactions: 83218 Sorted by model distance: nonbonded pdb=" OH TYR F 209 " pdb=" O ILE C 48 " model vdw 1.997 3.040 nonbonded pdb=" OG1 THR C 143 " pdb=" OE1 GLN C 152 " model vdw 2.007 3.040 nonbonded pdb=" OE2 GLU B 86 " pdb=" OG SER F 83 " model vdw 2.049 3.040 nonbonded pdb=" OE1 GLN C 61 " pdb=" OG SER C 65 " model vdw 2.106 3.040 nonbonded pdb=" OE1 GLU F 140 " pdb=" NE2 GLN F 150 " model vdw 2.131 3.120 ... (remaining 83213 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.010 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.002 0.026 10730 Z= 0.116 Angle : 0.411 5.860 14496 Z= 0.221 Chirality : 0.038 0.121 1659 Planarity : 0.003 0.036 1833 Dihedral : 17.023 116.332 4059 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 27.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 26.89 % Favored : 73.11 % 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: 0.86 (0.25), residues: 1320 helix: 2.26 (0.22), residues: 628 sheet: -0.97 (0.37), residues: 216 loop : -0.99 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.006 0.001 TYR G 266 PHE 0.008 0.001 PHE F 141 TRP 0.011 0.001 TRP G 250 HIS 0.002 0.000 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00246 (10730) covalent geometry : angle 0.41134 (14496) hydrogen bonds : bond 0.16471 ( 571) hydrogen bonds : angle 6.67858 ( 1677) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.372 Fit side-chains REVERT: C 59 GLN cc_start: 0.7306 (tt0) cc_final: 0.7020 (tt0) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1047 time to fit residues: 21.2116 Evaluate side-chains 145 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN B 128 HIS B 129 HIS G 158 HIS ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.162434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118935 restraints weight = 13793.625| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.26 r_work: 0.3354 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10730 Z= 0.154 Angle : 0.592 9.661 14496 Z= 0.303 Chirality : 0.043 0.150 1659 Planarity : 0.004 0.037 1833 Dihedral : 8.687 110.519 1632 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.56 % Allowed : 23.06 % Favored : 73.38 % 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: 0.68 (0.24), residues: 1320 helix: 2.00 (0.21), residues: 642 sheet: -0.76 (0.38), residues: 200 loop : -1.15 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 357 TYR 0.016 0.001 TYR C 51 PHE 0.020 0.001 PHE F 141 TRP 0.009 0.001 TRP F 338 HIS 0.005 0.001 HIS G 158 Details of bonding type rmsd covalent geometry : bond 0.00357 (10730) covalent geometry : angle 0.59188 (14496) hydrogen bonds : bond 0.04839 ( 571) hydrogen bonds : angle 5.02990 ( 1677) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.393 Fit side-chains REVERT: B 47 TYR cc_start: 0.8750 (m-10) cc_final: 0.8438 (m-80) REVERT: B 93 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8477 (mp) REVERT: B 98 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8728 (t0) REVERT: A 195 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7729 (t-90) REVERT: G 330 PHE cc_start: 0.5242 (OUTLIER) cc_final: 0.4702 (m-10) REVERT: F 232 TYR cc_start: 0.7976 (p90) cc_final: 0.7698 (p90) REVERT: F 238 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7603 (mpp) REVERT: C 76 GLU cc_start: 0.6190 (tm-30) cc_final: 0.5954 (tm-30) REVERT: C 113 LYS cc_start: 0.7496 (tptt) cc_final: 0.7278 (tptp) outliers start: 39 outliers final: 18 residues processed: 178 average time/residue: 0.0994 time to fit residues: 25.1229 Evaluate side-chains 156 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 258 ASP Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 94 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 92 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 0.0870 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 ASN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.162500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118599 restraints weight = 13823.489| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.30 r_work: 0.3331 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10730 Z= 0.164 Angle : 0.571 9.369 14496 Z= 0.294 Chirality : 0.043 0.150 1659 Planarity : 0.004 0.041 1833 Dihedral : 8.552 107.391 1632 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.74 % Allowed : 22.06 % Favored : 73.20 % 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: 0.68 (0.24), residues: 1320 helix: 1.93 (0.21), residues: 642 sheet: -0.37 (0.39), residues: 181 loop : -1.23 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 168 TYR 0.011 0.001 TYR C 51 PHE 0.016 0.001 PHE B 125 TRP 0.009 0.001 TRP F 338 HIS 0.003 0.001 HIS F 340 Details of bonding type rmsd covalent geometry : bond 0.00398 (10730) covalent geometry : angle 0.57140 (14496) hydrogen bonds : bond 0.04676 ( 571) hydrogen bonds : angle 4.79765 ( 1677) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 0.257 Fit side-chains REVERT: B 47 TYR cc_start: 0.8773 (m-10) cc_final: 0.8466 (m-80) REVERT: B 93 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8462 (mp) REVERT: B 98 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8724 (t0) REVERT: A 195 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7627 (t-90) REVERT: G 330 PHE cc_start: 0.5289 (OUTLIER) cc_final: 0.4816 (m-10) REVERT: F 227 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: F 232 TYR cc_start: 0.7998 (p90) cc_final: 0.7731 (p90) REVERT: F 276 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8605 (t) REVERT: F 329 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8261 (mttp) REVERT: C 59 GLN cc_start: 0.7815 (tt0) cc_final: 0.7562 (tm-30) REVERT: C 63 ASP cc_start: 0.6507 (p0) cc_final: 0.6255 (p0) REVERT: C 113 LYS cc_start: 0.7364 (tptt) cc_final: 0.7131 (tptp) outliers start: 52 outliers final: 30 residues processed: 179 average time/residue: 0.1087 time to fit residues: 27.1185 Evaluate side-chains 168 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 258 ASP Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 104 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 123 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS B 38 ASN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.163398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.119670 restraints weight = 13934.507| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.32 r_work: 0.3322 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10730 Z= 0.139 Angle : 0.538 7.614 14496 Z= 0.277 Chirality : 0.042 0.150 1659 Planarity : 0.004 0.041 1833 Dihedral : 8.366 102.560 1632 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.10 % Allowed : 21.60 % Favored : 73.29 % 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: 0.73 (0.24), residues: 1320 helix: 1.96 (0.21), residues: 642 sheet: -0.31 (0.38), residues: 191 loop : -1.21 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 16 TYR 0.013 0.001 TYR C 51 PHE 0.014 0.001 PHE B 125 TRP 0.009 0.001 TRP F 338 HIS 0.003 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00330 (10730) covalent geometry : angle 0.53777 (14496) hydrogen bonds : bond 0.04284 ( 571) hydrogen bonds : angle 4.54773 ( 1677) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 145 time to evaluate : 0.269 Fit side-chains REVERT: B 116 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8074 (pp20) REVERT: B 231 LYS cc_start: 0.7945 (tttt) cc_final: 0.7602 (mmtp) REVERT: B 232 GLU cc_start: 0.8244 (pt0) cc_final: 0.8029 (pt0) REVERT: A 64 GLU cc_start: 0.8527 (tt0) cc_final: 0.8180 (tp30) REVERT: A 195 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7579 (t-90) REVERT: A 231 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8395 (tttt) REVERT: G 330 PHE cc_start: 0.5306 (OUTLIER) cc_final: 0.4790 (m-10) REVERT: F 227 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: F 232 TYR cc_start: 0.8011 (p90) cc_final: 0.7776 (p90) REVERT: C 59 GLN cc_start: 0.7865 (tt0) cc_final: 0.7483 (tt0) REVERT: C 113 LYS cc_start: 0.7436 (tptt) cc_final: 0.7197 (tptp) REVERT: C 121 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.7052 (t70) outliers start: 56 outliers final: 34 residues processed: 186 average time/residue: 0.0983 time to fit residues: 26.0895 Evaluate side-chains 178 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 258 ASP Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 138 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 39 optimal weight: 0.0870 chunk 19 optimal weight: 0.0870 chunk 107 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 chunk 127 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 overall best weight: 0.4294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 38 ASN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.164510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120621 restraints weight = 13652.361| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.31 r_work: 0.3352 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10730 Z= 0.111 Angle : 0.515 6.971 14496 Z= 0.268 Chirality : 0.041 0.162 1659 Planarity : 0.004 0.040 1833 Dihedral : 8.136 99.521 1632 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.01 % Allowed : 21.79 % Favored : 74.20 % 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: 0.86 (0.24), residues: 1320 helix: 2.10 (0.21), residues: 640 sheet: -0.37 (0.37), residues: 201 loop : -1.14 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 16 TYR 0.007 0.001 TYR F 209 PHE 0.013 0.001 PHE F 141 TRP 0.009 0.001 TRP F 338 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00240 (10730) covalent geometry : angle 0.51545 (14496) hydrogen bonds : bond 0.03832 ( 571) hydrogen bonds : angle 4.34025 ( 1677) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.302 Fit side-chains REVERT: B 116 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7992 (pp20) REVERT: B 232 GLU cc_start: 0.8073 (pt0) cc_final: 0.7829 (pt0) REVERT: G 330 PHE cc_start: 0.4990 (OUTLIER) cc_final: 0.4455 (m-10) REVERT: F 141 PHE cc_start: 0.5806 (OUTLIER) cc_final: 0.5514 (p90) REVERT: F 208 ARG cc_start: 0.6625 (tpp-160) cc_final: 0.6372 (tpp-160) REVERT: F 227 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: F 329 LYS cc_start: 0.8454 (mtmm) cc_final: 0.8207 (mttm) REVERT: C 53 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6423 (mm-30) REVERT: C 59 GLN cc_start: 0.7717 (tt0) cc_final: 0.7275 (tt0) outliers start: 44 outliers final: 23 residues processed: 179 average time/residue: 0.1073 time to fit residues: 26.8657 Evaluate side-chains 167 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 138 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 76 optimal weight: 0.9980 chunk 41 optimal weight: 0.0270 chunk 42 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 129 optimal weight: 30.0000 chunk 124 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.166489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.124237 restraints weight = 13792.379| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.25 r_work: 0.3374 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10730 Z= 0.109 Angle : 0.509 8.264 14496 Z= 0.262 Chirality : 0.041 0.168 1659 Planarity : 0.004 0.040 1833 Dihedral : 7.986 97.175 1632 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.92 % Allowed : 21.79 % Favored : 74.29 % 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: 0.94 (0.24), residues: 1320 helix: 2.18 (0.21), residues: 640 sheet: -0.27 (0.39), residues: 193 loop : -1.14 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 16 TYR 0.006 0.001 TYR C 50 PHE 0.012 0.001 PHE F 141 TRP 0.010 0.001 TRP F 338 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00240 (10730) covalent geometry : angle 0.50888 (14496) hydrogen bonds : bond 0.03676 ( 571) hydrogen bonds : angle 4.20097 ( 1677) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.393 Fit side-chains REVERT: B 43 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8807 (t) REVERT: B 116 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8044 (pp20) REVERT: B 232 GLU cc_start: 0.8261 (pt0) cc_final: 0.7976 (pt0) REVERT: G 202 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8045 (mp0) REVERT: G 330 PHE cc_start: 0.5026 (OUTLIER) cc_final: 0.4525 (m-10) REVERT: F 141 PHE cc_start: 0.5830 (OUTLIER) cc_final: 0.5604 (p90) REVERT: F 227 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: C 59 GLN cc_start: 0.7897 (tt0) cc_final: 0.7419 (tt0) REVERT: C 121 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7092 (t70) outliers start: 43 outliers final: 30 residues processed: 179 average time/residue: 0.0881 time to fit residues: 22.4318 Evaluate side-chains 175 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 258 ASP Chi-restraints excluded: chain G residue 316 ILE Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 97 optimal weight: 0.0070 chunk 126 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.163416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119308 restraints weight = 13739.288| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.32 r_work: 0.3340 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10730 Z= 0.140 Angle : 0.535 8.986 14496 Z= 0.273 Chirality : 0.042 0.153 1659 Planarity : 0.004 0.040 1833 Dihedral : 8.037 95.399 1632 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.74 % Allowed : 22.06 % Favored : 74.20 % 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: 0.91 (0.24), residues: 1320 helix: 2.11 (0.21), residues: 640 sheet: -0.23 (0.38), residues: 203 loop : -1.15 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 16 TYR 0.017 0.001 TYR C 68 PHE 0.013 0.001 PHE B 125 TRP 0.008 0.001 TRP F 338 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00331 (10730) covalent geometry : angle 0.53489 (14496) hydrogen bonds : bond 0.04097 ( 571) hydrogen bonds : angle 4.24809 ( 1677) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.237 Fit side-chains REVERT: B 47 TYR cc_start: 0.8684 (m-10) cc_final: 0.8427 (m-80) REVERT: B 116 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8110 (pp20) REVERT: B 232 GLU cc_start: 0.8242 (pt0) cc_final: 0.7933 (pt0) REVERT: A 64 GLU cc_start: 0.8506 (tt0) cc_final: 0.8252 (tp30) REVERT: G 202 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8070 (mp0) REVERT: G 330 PHE cc_start: 0.4934 (OUTLIER) cc_final: 0.4439 (m-10) REVERT: F 227 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: C 59 GLN cc_start: 0.7936 (tt0) cc_final: 0.7537 (tt0) REVERT: C 61 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8329 (mt0) REVERT: C 121 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7073 (t70) outliers start: 41 outliers final: 33 residues processed: 169 average time/residue: 0.0923 time to fit residues: 22.0306 Evaluate side-chains 175 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 258 ASP Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.164693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.121194 restraints weight = 13764.446| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.31 r_work: 0.3351 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10730 Z= 0.127 Angle : 0.528 8.741 14496 Z= 0.270 Chirality : 0.041 0.152 1659 Planarity : 0.004 0.040 1833 Dihedral : 8.009 94.499 1632 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.01 % Allowed : 22.24 % Favored : 73.75 % 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: 0.92 (0.24), residues: 1320 helix: 2.14 (0.21), residues: 640 sheet: -0.17 (0.38), residues: 193 loop : -1.16 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 16 TYR 0.017 0.001 TYR C 68 PHE 0.011 0.001 PHE B 125 TRP 0.009 0.001 TRP F 338 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00295 (10730) covalent geometry : angle 0.52775 (14496) hydrogen bonds : bond 0.03950 ( 571) hydrogen bonds : angle 4.20103 ( 1677) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 140 time to evaluate : 0.355 Fit side-chains REVERT: B 47 TYR cc_start: 0.8690 (m-10) cc_final: 0.8428 (m-10) REVERT: B 116 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8110 (pp20) REVERT: A 64 GLU cc_start: 0.8437 (tt0) cc_final: 0.8219 (tp30) REVERT: G 202 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8056 (mp0) REVERT: G 330 PHE cc_start: 0.4884 (OUTLIER) cc_final: 0.4389 (m-10) REVERT: F 227 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: C 59 GLN cc_start: 0.8001 (tt0) cc_final: 0.7525 (tt0) outliers start: 44 outliers final: 36 residues processed: 171 average time/residue: 0.0922 time to fit residues: 22.3918 Evaluate side-chains 177 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 258 ASP Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 120 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN A 196 ASN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.164125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120546 restraints weight = 13849.524| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.30 r_work: 0.3343 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10730 Z= 0.139 Angle : 0.537 8.963 14496 Z= 0.276 Chirality : 0.042 0.164 1659 Planarity : 0.004 0.040 1833 Dihedral : 7.994 92.824 1632 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.56 % Allowed : 22.42 % Favored : 74.02 % 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: 0.91 (0.24), residues: 1320 helix: 2.10 (0.21), residues: 640 sheet: -0.14 (0.37), residues: 203 loop : -1.16 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 16 TYR 0.018 0.001 TYR C 68 PHE 0.012 0.001 PHE B 125 TRP 0.008 0.001 TRP F 338 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00328 (10730) covalent geometry : angle 0.53686 (14496) hydrogen bonds : bond 0.04059 ( 571) hydrogen bonds : angle 4.19937 ( 1677) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.384 Fit side-chains REVERT: B 47 TYR cc_start: 0.8691 (m-10) cc_final: 0.8421 (m-80) REVERT: B 116 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8121 (pp20) REVERT: B 232 GLU cc_start: 0.8270 (pt0) cc_final: 0.7956 (pt0) REVERT: G 202 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8067 (mp0) REVERT: G 330 PHE cc_start: 0.4814 (OUTLIER) cc_final: 0.4289 (m-10) REVERT: F 227 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: C 59 GLN cc_start: 0.7913 (tt0) cc_final: 0.7633 (tm-30) outliers start: 39 outliers final: 36 residues processed: 165 average time/residue: 0.1051 time to fit residues: 24.4765 Evaluate side-chains 174 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 258 ASP Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 39 optimal weight: 0.0470 chunk 114 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.165588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122500 restraints weight = 13653.524| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.26 r_work: 0.3371 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10730 Z= 0.111 Angle : 0.516 8.036 14496 Z= 0.266 Chirality : 0.040 0.157 1659 Planarity : 0.003 0.039 1833 Dihedral : 7.795 90.714 1632 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.65 % Allowed : 22.79 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.24), residues: 1320 helix: 2.20 (0.21), residues: 642 sheet: 0.02 (0.38), residues: 191 loop : -1.12 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 16 TYR 0.017 0.001 TYR C 68 PHE 0.011 0.001 PHE F 141 TRP 0.010 0.001 TRP G 250 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00246 (10730) covalent geometry : angle 0.51569 (14496) hydrogen bonds : bond 0.03609 ( 571) hydrogen bonds : angle 4.06299 ( 1677) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.455 Fit side-chains REVERT: B 43 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8790 (t) REVERT: B 116 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8149 (pp20) REVERT: B 232 GLU cc_start: 0.8250 (pt0) cc_final: 0.7918 (pt0) REVERT: G 202 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8047 (mp0) REVERT: G 330 PHE cc_start: 0.5055 (OUTLIER) cc_final: 0.4455 (m-10) REVERT: F 30 ARG cc_start: 0.7318 (mmm-85) cc_final: 0.7065 (mmm-85) REVERT: F 227 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: F 232 TYR cc_start: 0.7954 (p90) cc_final: 0.7539 (p90) REVERT: C 59 GLN cc_start: 0.7909 (tt0) cc_final: 0.7601 (tm-30) outliers start: 40 outliers final: 37 residues processed: 169 average time/residue: 0.1019 time to fit residues: 24.4469 Evaluate side-chains 176 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain A residue 13 TYR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 258 ASP Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 138 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.163483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119873 restraints weight = 13857.047| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.30 r_work: 0.3333 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10730 Z= 0.159 Angle : 0.557 9.876 14496 Z= 0.283 Chirality : 0.042 0.234 1659 Planarity : 0.004 0.039 1833 Dihedral : 7.899 89.524 1632 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.37 % Allowed : 22.97 % Favored : 73.66 % 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: 0.93 (0.24), residues: 1320 helix: 2.08 (0.21), residues: 640 sheet: -0.01 (0.37), residues: 201 loop : -1.15 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 16 TYR 0.018 0.001 TYR C 68 PHE 0.013 0.001 PHE B 125 TRP 0.008 0.001 TRP F 338 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00385 (10730) covalent geometry : angle 0.55653 (14496) hydrogen bonds : bond 0.04192 ( 571) hydrogen bonds : angle 4.19987 ( 1677) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.99 seconds wall clock time: 46 minutes 12.44 seconds (2772.44 seconds total)