Starting phenix.real_space_refine on Wed Mar 4 04:37:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tzf_26208/03_2026/7tzf_26208.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tzf_26208/03_2026/7tzf_26208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tzf_26208/03_2026/7tzf_26208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tzf_26208/03_2026/7tzf_26208.map" model { file = "/net/cci-nas-00/data/ceres_data/7tzf_26208/03_2026/7tzf_26208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tzf_26208/03_2026/7tzf_26208.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 72 5.16 5 C 6640 2.51 5 N 1733 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10342 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 755 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 106} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'PHE:plan': 2, 'ASP:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 90 Chain: "P" Number of atoms: 284 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Conformer: "C" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} bond proxies already assigned to first conformer: 265 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 3006 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1898 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2600 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} 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: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'P42': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 310 Unusual residues: {'NAG': 3, 'PLM': 11, 'Y01': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG P 18 " occ=0.50 ... (20 atoms not shown) pdb=" NH2CARG P 18 " occ=0.62 Time building chain proxies: 2.33, per 1000 atoms: 0.23 Number of scatterers: 10342 At special positions: 0 Unit cell: (84.5, 99.45, 163.15, 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 72 16.00 P 1 15.00 O 1896 8.00 N 1733 7.00 C 6640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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=1, symmetry=0 Links applied NAG-ASN " NAG E 201 " - " ASN E 71 " " NAG R 501 " - " ASN R 130 " " NAG R 502 " - " ASN R 73 " " NAG R 503 " - " ASN R 125 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 522.5 milliseconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 13 sheets defined 44.7% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'E' and resid 30 through 37 removed outlier: 4.046A pdb=" N LEU E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.803A pdb=" N LYS E 42 " --> pdb=" O PRO E 38 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 81 removed outlier: 3.809A pdb=" N GLU E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 101 removed outlier: 3.624A pdb=" N GLN E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 141 Proline residue: E 121 - end of helix Proline residue: E 126 - end of helix Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'R' and resid 42 through 62 removed outlier: 4.041A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 4.315A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.771A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.530A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.883A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 removed outlier: 3.529A pdb=" N THR R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix removed outlier: 3.619A pdb=" N THR R 330 " --> pdb=" O LYS R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 407 Processing helix chain 'A' and resid 12 through 40 removed outlier: 4.078A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.814A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.536A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.535A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.320A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.558A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.404A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.559A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.505A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'R' and resid 90 through 94 removed outlier: 3.734A pdb=" N LYS R 110 " --> pdb=" O SER R 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.346A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.580A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.554A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.692A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.547A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.576A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.053A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.716A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.829A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1441 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: 1.76 Time building geometry restraints manager: 1.19 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: 1664 1.32 - 1.44: 2888 1.44 - 1.57: 5888 1.57 - 1.69: 2 1.69 - 1.81: 102 Bond restraints: 10544 Sorted by residual: bond pdb=" N VAL P 32 " pdb=" CA VAL P 32 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.09e+01 bond pdb=" OBN P42 P 101 " pdb=" PBM P42 P 101 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" N THR P 36 " pdb=" CA THR P 36 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.27e-02 6.20e+03 6.67e+00 bond pdb=" CA SER P 34 " pdb=" CB SER P 34 " ideal model delta sigma weight residual 1.528 1.493 0.036 1.56e-02 4.11e+03 5.21e+00 bond pdb=" C4 P42 P 101 " pdb=" OBN P42 P 101 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.18e+00 ... (remaining 10539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 13896 1.46 - 2.91: 316 2.91 - 4.37: 31 4.37 - 5.83: 10 5.83 - 7.28: 2 Bond angle restraints: 14255 Sorted by residual: angle pdb=" CA GLY P 33 " pdb=" C GLY P 33 " pdb=" O GLY P 33 " ideal model delta sigma weight residual 121.92 118.21 3.71 1.05e+00 9.07e-01 1.25e+01 angle pdb=" CA THR P 36 " pdb=" C THR P 36 " pdb=" O THR P 36 " ideal model delta sigma weight residual 121.88 118.40 3.48 1.13e+00 7.83e-01 9.50e+00 angle pdb=" CA SER P 34 " pdb=" C SER P 34 " pdb=" O SER P 34 " ideal model delta sigma weight residual 120.55 117.75 2.80 1.06e+00 8.90e-01 6.99e+00 angle pdb=" C LEU E 119 " pdb=" N ILE E 120 " pdb=" CA ILE E 120 " ideal model delta sigma weight residual 120.33 122.29 -1.96 8.00e-01 1.56e+00 6.02e+00 angle pdb=" CA VAL P 32 " pdb=" C VAL P 32 " pdb=" O VAL P 32 " ideal model delta sigma weight residual 120.78 118.05 2.73 1.25e+00 6.40e-01 4.78e+00 ... (remaining 14250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.81: 6133 25.81 - 51.62: 272 51.62 - 77.42: 41 77.42 - 103.23: 9 103.23 - 129.04: 3 Dihedral angle restraints: 6458 sinusoidal: 2746 harmonic: 3712 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 172.70 -79.70 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 169.23 -76.23 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -32.98 -53.02 1 1.00e+01 1.00e-02 3.83e+01 ... (remaining 6455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1276 0.050 - 0.100: 246 0.100 - 0.150: 54 0.150 - 0.199: 1 0.199 - 0.249: 1 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CA TYR P 37 " pdb=" N TYR P 37 " pdb=" C TYR P 37 " pdb=" CB TYR P 37 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CBE P42 P 101 " pdb=" CAB P42 P 101 " pdb=" CBK P42 P 101 " pdb=" OBD P42 P 101 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CBF Y01 R 507 " pdb=" CAS Y01 R 507 " pdb=" CBD Y01 R 507 " pdb=" CBH Y01 R 507 " both_signs ideal model delta sigma weight residual False -2.45 -2.59 0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 1575 not shown) Planarity restraints: 1790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN P 31 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C ASN P 31 " -0.037 2.00e-02 2.50e+03 pdb=" O ASN P 31 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL P 32 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN P 35 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ASN P 35 " -0.023 2.00e-02 2.50e+03 pdb=" O ASN P 35 " 0.008 2.00e-02 2.50e+03 pdb=" N THR P 36 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 236 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 ... (remaining 1787 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2322 2.78 - 3.31: 9517 3.31 - 3.84: 17592 3.84 - 4.37: 21836 4.37 - 4.90: 35982 Nonbonded interactions: 87249 Sorted by model distance: nonbonded pdb=" O LEU P 16 " pdb=" OG SER P 20 " model vdw 2.252 3.040 nonbonded pdb=" O TYR R 374 " pdb=" OG SER R 378 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.263 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.284 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.285 3.040 ... (remaining 87244 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.460 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: 0.000 Load rotamer database and sin/cos tables:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.004 0.106 10558 Z= 0.213 Angle : 0.536 7.284 14285 Z= 0.297 Chirality : 0.041 0.249 1578 Planarity : 0.003 0.032 1786 Dihedral : 14.486 129.040 4035 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.43 % Allowed : 11.76 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.21), residues: 1257 helix: -2.10 (0.18), residues: 493 sheet: -0.34 (0.32), residues: 237 loop : -1.42 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 98 TYR 0.010 0.001 TYR R 391 PHE 0.011 0.001 PHE B 151 TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00367 (10544) covalent geometry : angle 0.52934 (14255) SS BOND : bond 0.00232 ( 9) SS BOND : angle 0.89289 ( 18) hydrogen bonds : bond 0.23125 ( 503) hydrogen bonds : angle 8.24202 ( 1441) Misc. bond : bond 0.10561 ( 1) link_NAG-ASN : bond 0.00287 ( 4) link_NAG-ASN : angle 2.83866 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: P 11 ARG cc_start: 0.8475 (mtm-85) cc_final: 0.8186 (mtm-85) REVERT: P 15 PHE cc_start: 0.8283 (t80) cc_final: 0.8066 (t80) REVERT: R 99 PHE cc_start: 0.5097 (m-80) cc_final: 0.4885 (m-10) REVERT: R 141 LYS cc_start: 0.6809 (tttt) cc_final: 0.6605 (mtmt) REVERT: R 338 TYR cc_start: 0.5831 (m-80) cc_final: 0.5349 (m-10) REVERT: A 209 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: A 296 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7280 (mp) REVERT: B 46 ARG cc_start: 0.6580 (mtp85) cc_final: 0.6202 (mmm-85) REVERT: B 96 ARG cc_start: 0.7217 (mtp-110) cc_final: 0.6985 (ttp-170) REVERT: B 134 ARG cc_start: 0.6994 (ptt90) cc_final: 0.6791 (ptt90) REVERT: B 197 ARG cc_start: 0.7020 (mmm-85) cc_final: 0.6788 (mmt90) REVERT: B 268 ASN cc_start: 0.7287 (p0) cc_final: 0.7058 (p0) REVERT: G 16 VAL cc_start: 0.7614 (t) cc_final: 0.7342 (m) REVERT: N 1 GLN cc_start: 0.7579 (tp-100) cc_final: 0.7364 (tp40) REVERT: N 33 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8371 (ttpt) outliers start: 15 outliers final: 5 residues processed: 189 average time/residue: 0.7012 time to fit residues: 140.0482 Evaluate side-chains 151 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 HIS ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 ASN P 31 ASN P 35 ASN R 52 GLN R 93 GLN R 184 HIS ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 288 ASN R 336 HIS R 399 GLN A 35 GLN A 59 GLN A 254 ASN A 357 HIS B 6 GLN B 35 ASN B 75 GLN B 176 GLN B 340 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.178898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120574 restraints weight = 16499.098| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.26 r_work: 0.3205 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10558 Z= 0.134 Angle : 0.560 8.551 14285 Z= 0.297 Chirality : 0.042 0.138 1578 Planarity : 0.004 0.038 1786 Dihedral : 8.987 127.897 1825 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.01 % Allowed : 14.91 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1257 helix: 0.32 (0.22), residues: 495 sheet: 0.10 (0.33), residues: 223 loop : -1.04 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 214 TYR 0.012 0.001 TYR R 131 PHE 0.016 0.002 PHE E 69 TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00279 (10544) covalent geometry : angle 0.55409 (14255) SS BOND : bond 0.00204 ( 9) SS BOND : angle 0.60109 ( 18) hydrogen bonds : bond 0.04951 ( 503) hydrogen bonds : angle 5.09255 ( 1441) Misc. bond : bond 0.00026 ( 1) link_NAG-ASN : bond 0.00377 ( 4) link_NAG-ASN : angle 2.93871 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.379 Fit side-chains REVERT: P 10 GLN cc_start: 0.7885 (mp-120) cc_final: 0.7561 (mm-40) REVERT: P 11 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8296 (mtm-85) REVERT: P 15 PHE cc_start: 0.8331 (t80) cc_final: 0.8045 (t80) REVERT: R 141 LYS cc_start: 0.6826 (tttt) cc_final: 0.6359 (mtmt) REVERT: R 271 LEU cc_start: 0.7528 (mt) cc_final: 0.7188 (mt) REVERT: A 21 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5944 (tm-30) REVERT: A 209 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7367 (mp0) REVERT: B 13 GLN cc_start: 0.7280 (mm-40) cc_final: 0.6838 (tm-30) REVERT: B 46 ARG cc_start: 0.7445 (mtp85) cc_final: 0.6730 (mmm-85) REVERT: B 134 ARG cc_start: 0.7394 (ptt90) cc_final: 0.7166 (ptt90) REVERT: B 137 ARG cc_start: 0.8250 (tpp-160) cc_final: 0.7868 (tpt170) REVERT: G 20 LYS cc_start: 0.7240 (mttm) cc_final: 0.7033 (mttm) REVERT: N 33 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8729 (ttmt) REVERT: N 105 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7164 (mtm110) REVERT: N 114 THR cc_start: 0.7975 (p) cc_final: 0.7710 (p) outliers start: 21 outliers final: 6 residues processed: 167 average time/residue: 0.6654 time to fit residues: 117.9719 Evaluate side-chains 153 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 30 optimal weight: 0.0370 chunk 40 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 233 ASN R 286 ASN R 318 ASN R 399 GLN A 35 GLN A 59 GLN B 35 ASN N 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.177793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120093 restraints weight = 21830.963| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.62 r_work: 0.3169 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10558 Z= 0.152 Angle : 0.569 7.059 14285 Z= 0.300 Chirality : 0.043 0.191 1578 Planarity : 0.004 0.039 1786 Dihedral : 9.343 130.279 1818 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.06 % Allowed : 14.72 % Favored : 82.22 % 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: 0.13 (0.23), residues: 1257 helix: 1.06 (0.23), residues: 495 sheet: 0.27 (0.33), residues: 223 loop : -0.86 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 96 TYR 0.012 0.002 TYR E 66 PHE 0.014 0.002 PHE B 151 TRP 0.019 0.002 TRP A 234 HIS 0.007 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00332 (10544) covalent geometry : angle 0.56237 (14255) SS BOND : bond 0.00514 ( 9) SS BOND : angle 0.91754 ( 18) hydrogen bonds : bond 0.04898 ( 503) hydrogen bonds : angle 4.85354 ( 1441) Misc. bond : bond 0.00005 ( 1) link_NAG-ASN : bond 0.00241 ( 4) link_NAG-ASN : angle 2.98431 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: P 11 ARG cc_start: 0.8682 (mtm-85) cc_final: 0.8289 (mtm-85) REVERT: R 271 LEU cc_start: 0.7570 (mt) cc_final: 0.7260 (mt) REVERT: R 332 GLU cc_start: 0.5839 (mm-30) cc_final: 0.5323 (mt-10) REVERT: R 338 TYR cc_start: 0.5989 (m-10) cc_final: 0.5386 (m-80) REVERT: R 364 SER cc_start: 0.6790 (OUTLIER) cc_final: 0.6509 (t) REVERT: R 396 ASN cc_start: 0.7129 (OUTLIER) cc_final: 0.6779 (t0) REVERT: A 21 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.6025 (tm-30) REVERT: A 209 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7585 (mp0) REVERT: B 46 ARG cc_start: 0.7442 (mtp85) cc_final: 0.6743 (mmm-85) REVERT: B 134 ARG cc_start: 0.7443 (ptt90) cc_final: 0.7216 (ptt90) REVERT: B 137 ARG cc_start: 0.8289 (tpp-160) cc_final: 0.7945 (tpt170) REVERT: G 20 LYS cc_start: 0.7188 (mttm) cc_final: 0.6927 (mttm) REVERT: G 21 MET cc_start: 0.7428 (tpp) cc_final: 0.7172 (mmm) REVERT: N 33 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8692 (ttmt) REVERT: N 39 GLN cc_start: 0.8971 (tt0) cc_final: 0.8728 (tt0) REVERT: N 105 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7191 (mtm110) outliers start: 32 outliers final: 10 residues processed: 172 average time/residue: 0.6665 time to fit residues: 121.4505 Evaluate side-chains 162 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain R residue 396 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 119 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.179319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141020 restraints weight = 22844.577| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 4.99 r_work: 0.3095 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10558 Z= 0.106 Angle : 0.497 6.595 14285 Z= 0.262 Chirality : 0.041 0.140 1578 Planarity : 0.003 0.039 1786 Dihedral : 8.663 123.614 1817 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.49 % Allowed : 16.16 % Favored : 81.36 % 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: 0.56 (0.23), residues: 1257 helix: 1.61 (0.23), residues: 495 sheet: 0.27 (0.32), residues: 224 loop : -0.73 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.010 0.001 TYR A 339 PHE 0.012 0.001 PHE A 212 TRP 0.017 0.001 TRP A 234 HIS 0.003 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00222 (10544) covalent geometry : angle 0.49024 (14255) SS BOND : bond 0.00170 ( 9) SS BOND : angle 0.87479 ( 18) hydrogen bonds : bond 0.03965 ( 503) hydrogen bonds : angle 4.50366 ( 1441) Misc. bond : bond 0.00005 ( 1) link_NAG-ASN : bond 0.00261 ( 4) link_NAG-ASN : angle 2.82238 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7861 (mp-120) cc_final: 0.7413 (mm-40) REVERT: P 11 ARG cc_start: 0.8580 (mtm-85) cc_final: 0.8181 (mtm-85) REVERT: R 49 MET cc_start: 0.2844 (mmp) cc_final: 0.2533 (mmt) REVERT: R 271 LEU cc_start: 0.7518 (mt) cc_final: 0.7204 (mt) REVERT: R 332 GLU cc_start: 0.5863 (OUTLIER) cc_final: 0.5450 (mt-10) REVERT: R 338 TYR cc_start: 0.5904 (m-10) cc_final: 0.5345 (m-80) REVERT: R 364 SER cc_start: 0.6747 (OUTLIER) cc_final: 0.6497 (t) REVERT: R 396 ASN cc_start: 0.7054 (t0) cc_final: 0.6706 (t0) REVERT: A 20 ARG cc_start: 0.6889 (mtm-85) cc_final: 0.6580 (mtm110) REVERT: A 21 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5943 (tm-30) REVERT: A 209 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7322 (mp0) REVERT: A 314 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6828 (pt0) REVERT: B 46 ARG cc_start: 0.7305 (mtp85) cc_final: 0.6560 (mmm-85) REVERT: B 96 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7895 (ttp-170) REVERT: B 137 ARG cc_start: 0.8270 (tpp-160) cc_final: 0.7869 (tpt170) REVERT: G 20 LYS cc_start: 0.7183 (mttm) cc_final: 0.6964 (mttm) REVERT: G 21 MET cc_start: 0.7432 (tpp) cc_final: 0.7146 (mmm) REVERT: G 58 GLU cc_start: 0.5541 (mm-30) cc_final: 0.5308 (mm-30) REVERT: N 39 GLN cc_start: 0.8943 (tt0) cc_final: 0.8709 (tt0) outliers start: 26 outliers final: 7 residues processed: 172 average time/residue: 0.6663 time to fit residues: 121.4398 Evaluate side-chains 159 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 399 GLN A 59 GLN A 390 GLN B 35 ASN N 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.177443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122187 restraints weight = 20665.535| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.61 r_work: 0.3196 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10558 Z= 0.132 Angle : 0.540 6.883 14285 Z= 0.283 Chirality : 0.042 0.141 1578 Planarity : 0.004 0.038 1786 Dihedral : 9.055 124.451 1817 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.49 % Allowed : 16.83 % Favored : 80.69 % 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: 0.62 (0.23), residues: 1257 helix: 1.66 (0.23), residues: 503 sheet: 0.23 (0.33), residues: 227 loop : -0.69 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 96 TYR 0.013 0.001 TYR N 80 PHE 0.013 0.001 PHE B 151 TRP 0.018 0.001 TRP A 234 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00286 (10544) covalent geometry : angle 0.53252 (14255) SS BOND : bond 0.00204 ( 9) SS BOND : angle 1.14457 ( 18) hydrogen bonds : bond 0.04285 ( 503) hydrogen bonds : angle 4.57834 ( 1441) Misc. bond : bond 0.00008 ( 1) link_NAG-ASN : bond 0.00250 ( 4) link_NAG-ASN : angle 2.90149 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: P 11 ARG cc_start: 0.8646 (mtm-85) cc_final: 0.8419 (mtm-85) REVERT: R 49 MET cc_start: 0.2992 (mmp) cc_final: 0.2680 (mmt) REVERT: R 213 ARG cc_start: 0.5867 (tpp-160) cc_final: 0.5543 (mtp180) REVERT: R 271 LEU cc_start: 0.7579 (mt) cc_final: 0.7348 (mt) REVERT: R 332 GLU cc_start: 0.5840 (OUTLIER) cc_final: 0.5612 (mt-10) REVERT: R 338 TYR cc_start: 0.6027 (m-10) cc_final: 0.5488 (m-80) REVERT: R 396 ASN cc_start: 0.7077 (OUTLIER) cc_final: 0.6710 (t0) REVERT: A 21 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.6012 (tm-30) REVERT: A 209 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: A 311 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7033 (m-10) REVERT: A 314 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6935 (pt0) REVERT: B 44 GLN cc_start: 0.5525 (mm-40) cc_final: 0.5184 (mm-40) REVERT: B 46 ARG cc_start: 0.7406 (mtp85) cc_final: 0.6695 (mmm-85) REVERT: B 137 ARG cc_start: 0.8266 (tpp-160) cc_final: 0.7899 (tpt170) REVERT: G 20 LYS cc_start: 0.7232 (mttm) cc_final: 0.6997 (mttm) REVERT: N 39 GLN cc_start: 0.8954 (tt0) cc_final: 0.8669 (tt0) REVERT: N 114 THR cc_start: 0.8002 (p) cc_final: 0.7791 (p) outliers start: 26 outliers final: 12 residues processed: 167 average time/residue: 0.6914 time to fit residues: 122.1199 Evaluate side-chains 164 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 396 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 399 GLN A 59 GLN A 390 GLN N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.176201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119108 restraints weight = 14197.440| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.10 r_work: 0.3169 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10558 Z= 0.193 Angle : 0.633 8.071 14285 Z= 0.332 Chirality : 0.045 0.159 1578 Planarity : 0.004 0.042 1786 Dihedral : 10.613 121.495 1817 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.87 % Allowed : 17.02 % Favored : 80.11 % 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: 0.37 (0.23), residues: 1257 helix: 1.27 (0.23), residues: 506 sheet: 0.22 (0.33), residues: 226 loop : -0.71 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 96 TYR 0.013 0.002 TYR E 66 PHE 0.016 0.002 PHE B 151 TRP 0.021 0.002 TRP A 234 HIS 0.008 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00429 (10544) covalent geometry : angle 0.62386 (14255) SS BOND : bond 0.00334 ( 9) SS BOND : angle 1.58658 ( 18) hydrogen bonds : bond 0.05028 ( 503) hydrogen bonds : angle 4.86876 ( 1441) Misc. bond : bond 0.00004 ( 1) link_NAG-ASN : bond 0.00306 ( 4) link_NAG-ASN : angle 3.22719 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.362 Fit side-chains REVERT: P 11 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8393 (mtm-85) REVERT: R 49 MET cc_start: 0.3015 (mmp) cc_final: 0.2683 (mmt) REVERT: R 141 LYS cc_start: 0.6703 (tttt) cc_final: 0.6390 (mtmt) REVERT: R 158 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7340 (tp) REVERT: R 213 ARG cc_start: 0.5841 (tpp-160) cc_final: 0.5517 (mpp-170) REVERT: R 332 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5692 (mt-10) REVERT: R 338 TYR cc_start: 0.5934 (m-10) cc_final: 0.5533 (m-10) REVERT: R 396 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6660 (t0) REVERT: R 405 GLN cc_start: 0.6571 (mp10) cc_final: 0.6343 (mp10) REVERT: A 209 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: A 311 TYR cc_start: 0.7798 (OUTLIER) cc_final: 0.6984 (m-10) REVERT: B 13 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6857 (tm-30) REVERT: B 44 GLN cc_start: 0.5489 (mm-40) cc_final: 0.5169 (mm-40) REVERT: B 46 ARG cc_start: 0.7490 (mtp85) cc_final: 0.6750 (mmm-85) REVERT: B 137 ARG cc_start: 0.8210 (tpp-160) cc_final: 0.7849 (tpt170) REVERT: B 172 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7540 (mt-10) REVERT: N 39 GLN cc_start: 0.8982 (tt0) cc_final: 0.8751 (tt0) REVERT: N 114 THR cc_start: 0.8016 (p) cc_final: 0.7770 (p) outliers start: 30 outliers final: 16 residues processed: 167 average time/residue: 0.6906 time to fit residues: 122.1436 Evaluate side-chains 162 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 396 ASN Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain N residue 30 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 50 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 399 GLN A 59 GLN B 35 ASN N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.178948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122473 restraints weight = 19453.207| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.53 r_work: 0.3205 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10558 Z= 0.103 Angle : 0.498 6.663 14285 Z= 0.262 Chirality : 0.041 0.146 1578 Planarity : 0.003 0.041 1786 Dihedral : 9.113 112.343 1815 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.29 % Allowed : 17.02 % Favored : 80.69 % 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: 0.74 (0.24), residues: 1257 helix: 1.77 (0.23), residues: 506 sheet: 0.24 (0.33), residues: 223 loop : -0.64 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.011 0.001 TYR R 149 PHE 0.014 0.001 PHE A 212 TRP 0.019 0.001 TRP A 234 HIS 0.003 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00214 (10544) covalent geometry : angle 0.49134 (14255) SS BOND : bond 0.00166 ( 9) SS BOND : angle 0.89450 ( 18) hydrogen bonds : bond 0.03811 ( 503) hydrogen bonds : angle 4.47310 ( 1441) Misc. bond : bond 0.00007 ( 1) link_NAG-ASN : bond 0.00267 ( 4) link_NAG-ASN : angle 2.78717 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.372 Fit side-chains REVERT: P 10 GLN cc_start: 0.7872 (mp-120) cc_final: 0.7458 (mm-40) REVERT: P 11 ARG cc_start: 0.8646 (mtm-85) cc_final: 0.8219 (mtm-85) REVERT: R 49 MET cc_start: 0.3028 (mmp) cc_final: 0.2707 (mmt) REVERT: R 141 LYS cc_start: 0.6661 (tttt) cc_final: 0.6332 (mtmt) REVERT: R 213 ARG cc_start: 0.5877 (tpp-160) cc_final: 0.5575 (mtp180) REVERT: R 271 LEU cc_start: 0.7515 (mt) cc_final: 0.7301 (mt) REVERT: R 332 GLU cc_start: 0.5917 (OUTLIER) cc_final: 0.5617 (mt-10) REVERT: R 338 TYR cc_start: 0.5954 (m-10) cc_final: 0.5578 (m-10) REVERT: R 396 ASN cc_start: 0.7009 (OUTLIER) cc_final: 0.6585 (t0) REVERT: A 21 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6001 (tm-30) REVERT: A 50 GLU cc_start: 0.5022 (OUTLIER) cc_final: 0.4682 (mp0) REVERT: A 209 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7383 (mp0) REVERT: B 44 GLN cc_start: 0.5474 (mm-40) cc_final: 0.5156 (mm-40) REVERT: B 46 ARG cc_start: 0.7366 (mtp85) cc_final: 0.6628 (mmm-85) REVERT: B 137 ARG cc_start: 0.8240 (tpp-160) cc_final: 0.7866 (tpt170) REVERT: N 39 GLN cc_start: 0.8945 (tt0) cc_final: 0.8702 (tt0) REVERT: N 89 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6869 (pm20) REVERT: N 114 THR cc_start: 0.8014 (p) cc_final: 0.7780 (p) outliers start: 24 outliers final: 9 residues processed: 155 average time/residue: 0.6728 time to fit residues: 110.5663 Evaluate side-chains 149 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 396 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 89 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 79 optimal weight: 0.0470 chunk 73 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 59 GLN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.177826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122677 restraints weight = 19658.458| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.64 r_work: 0.3181 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10558 Z= 0.126 Angle : 0.532 7.007 14285 Z= 0.278 Chirality : 0.042 0.142 1578 Planarity : 0.004 0.040 1786 Dihedral : 9.157 110.244 1815 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.20 % Allowed : 17.21 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.24), residues: 1257 helix: 1.76 (0.23), residues: 508 sheet: 0.24 (0.33), residues: 225 loop : -0.63 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.010 0.001 TYR A 339 PHE 0.012 0.001 PHE B 151 TRP 0.018 0.001 TRP A 234 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00274 (10544) covalent geometry : angle 0.52405 (14255) SS BOND : bond 0.00213 ( 9) SS BOND : angle 1.11262 ( 18) hydrogen bonds : bond 0.04094 ( 503) hydrogen bonds : angle 4.54092 ( 1441) Misc. bond : bond 0.00010 ( 1) link_NAG-ASN : bond 0.00276 ( 4) link_NAG-ASN : angle 2.86629 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7895 (mp-120) cc_final: 0.7495 (mm-40) REVERT: P 11 ARG cc_start: 0.8642 (mtm-85) cc_final: 0.8399 (mtm-85) REVERT: R 49 MET cc_start: 0.3082 (mmp) cc_final: 0.2765 (mmt) REVERT: R 158 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7230 (tp) REVERT: R 213 ARG cc_start: 0.5867 (tpp-160) cc_final: 0.5551 (mtp180) REVERT: R 271 LEU cc_start: 0.7560 (mt) cc_final: 0.7326 (mt) REVERT: R 332 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5561 (mt-10) REVERT: R 338 TYR cc_start: 0.5941 (m-10) cc_final: 0.5568 (m-10) REVERT: R 396 ASN cc_start: 0.7041 (OUTLIER) cc_final: 0.6637 (t0) REVERT: A 21 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.6014 (tm-30) REVERT: A 50 GLU cc_start: 0.5066 (OUTLIER) cc_final: 0.4739 (mp0) REVERT: A 209 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: A 311 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7002 (m-10) REVERT: B 13 GLN cc_start: 0.7427 (mm-40) cc_final: 0.6912 (tm-30) REVERT: B 44 GLN cc_start: 0.5522 (mm-40) cc_final: 0.5207 (mm-40) REVERT: B 46 ARG cc_start: 0.7403 (mtp85) cc_final: 0.6660 (mmm-85) REVERT: B 137 ARG cc_start: 0.8260 (tpp-160) cc_final: 0.7901 (tpt170) REVERT: N 39 GLN cc_start: 0.8972 (tt0) cc_final: 0.8731 (tt0) REVERT: N 89 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6880 (pm20) REVERT: N 114 THR cc_start: 0.8008 (p) cc_final: 0.7775 (p) outliers start: 23 outliers final: 10 residues processed: 154 average time/residue: 0.6773 time to fit residues: 110.4344 Evaluate side-chains 155 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 396 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 89 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.176880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122964 restraints weight = 16140.621| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.16 r_work: 0.3208 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10558 Z= 0.136 Angle : 0.550 7.211 14285 Z= 0.288 Chirality : 0.042 0.141 1578 Planarity : 0.004 0.056 1786 Dihedral : 9.367 108.891 1815 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.20 % Allowed : 17.02 % Favored : 80.78 % 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: 0.70 (0.24), residues: 1257 helix: 1.75 (0.23), residues: 499 sheet: 0.24 (0.33), residues: 226 loop : -0.64 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.010 0.001 TYR R 391 PHE 0.013 0.001 PHE B 151 TRP 0.019 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00298 (10544) covalent geometry : angle 0.54232 (14255) SS BOND : bond 0.00239 ( 9) SS BOND : angle 1.15715 ( 18) hydrogen bonds : bond 0.04254 ( 503) hydrogen bonds : angle 4.61022 ( 1441) Misc. bond : bond 0.00003 ( 1) link_NAG-ASN : bond 0.00281 ( 4) link_NAG-ASN : angle 2.91396 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: E 111 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6134 (mp) REVERT: P 11 ARG cc_start: 0.8616 (mtm-85) cc_final: 0.8369 (mtm-85) REVERT: R 49 MET cc_start: 0.3082 (mmp) cc_final: 0.2768 (mmt) REVERT: R 213 ARG cc_start: 0.5867 (tpp-160) cc_final: 0.5568 (mtp180) REVERT: R 271 LEU cc_start: 0.7603 (mt) cc_final: 0.7396 (mt) REVERT: R 332 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.5581 (mt-10) REVERT: R 338 TYR cc_start: 0.5918 (m-10) cc_final: 0.5615 (m-10) REVERT: R 396 ASN cc_start: 0.7064 (OUTLIER) cc_final: 0.6683 (t0) REVERT: A 21 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5998 (tm-30) REVERT: A 209 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: A 215 ASP cc_start: 0.7566 (m-30) cc_final: 0.7215 (m-30) REVERT: A 311 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.6991 (m-10) REVERT: B 13 GLN cc_start: 0.7408 (mm-40) cc_final: 0.6922 (tm-30) REVERT: B 44 GLN cc_start: 0.5518 (mm-40) cc_final: 0.5189 (mm-40) REVERT: B 46 ARG cc_start: 0.7371 (mtp85) cc_final: 0.6649 (mmm-85) REVERT: B 96 ARG cc_start: 0.8344 (mtp-110) cc_final: 0.7943 (ttp-170) REVERT: B 137 ARG cc_start: 0.8224 (tpp-160) cc_final: 0.7877 (tpt170) REVERT: N 39 GLN cc_start: 0.8938 (tt0) cc_final: 0.8679 (tt0) REVERT: N 89 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: N 114 THR cc_start: 0.7994 (p) cc_final: 0.7757 (p) outliers start: 23 outliers final: 11 residues processed: 154 average time/residue: 0.6882 time to fit residues: 112.2772 Evaluate side-chains 157 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain R residue 396 ASN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 26 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 95 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 94 optimal weight: 0.0770 chunk 13 optimal weight: 0.0370 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 35 GLN A 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.180068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127687 restraints weight = 14561.965| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.20 r_work: 0.3257 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10558 Z= 0.098 Angle : 0.487 6.137 14285 Z= 0.256 Chirality : 0.040 0.145 1578 Planarity : 0.003 0.049 1786 Dihedral : 8.410 99.729 1815 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.53 % Allowed : 17.50 % Favored : 80.98 % 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: 1257 helix: 2.01 (0.23), residues: 503 sheet: 0.28 (0.33), residues: 212 loop : -0.54 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.011 0.001 TYR R 149 PHE 0.013 0.001 PHE A 212 TRP 0.019 0.001 TRP A 234 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00208 (10544) covalent geometry : angle 0.48073 (14255) SS BOND : bond 0.00163 ( 9) SS BOND : angle 0.75068 ( 18) hydrogen bonds : bond 0.03527 ( 503) hydrogen bonds : angle 4.37412 ( 1441) Misc. bond : bond 0.00009 ( 1) link_NAG-ASN : bond 0.00283 ( 4) link_NAG-ASN : angle 2.61525 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: E 136 LEU cc_start: 0.7287 (tp) cc_final: 0.7054 (tp) REVERT: P 10 GLN cc_start: 0.7823 (mp-120) cc_final: 0.7396 (mm-40) REVERT: P 11 ARG cc_start: 0.8599 (mtm-85) cc_final: 0.8132 (mtm-85) REVERT: R 49 MET cc_start: 0.3022 (mmp) cc_final: 0.2701 (mmt) REVERT: R 213 ARG cc_start: 0.5853 (tpp-160) cc_final: 0.5583 (mtp180) REVERT: R 271 LEU cc_start: 0.7542 (mt) cc_final: 0.7327 (mt) REVERT: R 332 GLU cc_start: 0.5991 (OUTLIER) cc_final: 0.5588 (mt-10) REVERT: R 338 TYR cc_start: 0.5912 (m-10) cc_final: 0.5582 (m-10) REVERT: R 382 PHE cc_start: 0.7537 (m-80) cc_final: 0.7321 (m-80) REVERT: A 21 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5976 (tm-30) REVERT: A 209 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7289 (mp0) REVERT: A 215 ASP cc_start: 0.7558 (m-30) cc_final: 0.7214 (m-30) REVERT: B 44 GLN cc_start: 0.5467 (mm-40) cc_final: 0.5158 (mm-40) REVERT: B 46 ARG cc_start: 0.7251 (mtp85) cc_final: 0.6528 (mmm-85) REVERT: B 96 ARG cc_start: 0.8303 (mtp-110) cc_final: 0.7902 (ttp-170) REVERT: B 130 GLU cc_start: 0.4194 (mt-10) cc_final: 0.3923 (mp0) REVERT: B 137 ARG cc_start: 0.8178 (tpp-160) cc_final: 0.7843 (tpt170) REVERT: N 39 GLN cc_start: 0.8899 (tt0) cc_final: 0.8656 (tt0) REVERT: N 89 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: N 114 THR cc_start: 0.7956 (p) cc_final: 0.7744 (p) outliers start: 16 outliers final: 10 residues processed: 153 average time/residue: 0.6703 time to fit residues: 108.9062 Evaluate side-chains 155 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 332 GLU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN A 35 GLN A 59 GLN A 390 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.178331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124409 restraints weight = 14579.392| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.10 r_work: 0.3229 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10558 Z= 0.120 Angle : 0.520 6.683 14285 Z= 0.272 Chirality : 0.041 0.142 1578 Planarity : 0.004 0.042 1786 Dihedral : 8.664 96.897 1815 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.34 % Allowed : 18.26 % Favored : 80.40 % 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: 0.89 (0.24), residues: 1257 helix: 1.93 (0.23), residues: 503 sheet: 0.30 (0.33), residues: 223 loop : -0.55 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 214 TYR 0.009 0.001 TYR R 150 PHE 0.012 0.001 PHE B 151 TRP 0.018 0.001 TRP A 234 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00260 (10544) covalent geometry : angle 0.51322 (14255) SS BOND : bond 0.00204 ( 9) SS BOND : angle 0.99199 ( 18) hydrogen bonds : bond 0.03911 ( 503) hydrogen bonds : angle 4.46758 ( 1441) Misc. bond : bond 0.00009 ( 1) link_NAG-ASN : bond 0.00263 ( 4) link_NAG-ASN : angle 2.76338 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5713.68 seconds wall clock time: 97 minutes 34.58 seconds (5854.58 seconds total)