Starting phenix.real_space_refine on Thu Jun 4 22:14:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjz_60161/06_2026/8zjz_60161.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjz_60161/06_2026/8zjz_60161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zjz_60161/06_2026/8zjz_60161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjz_60161/06_2026/8zjz_60161.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjz_60161/06_2026/8zjz_60161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjz_60161/06_2026/8zjz_60161.cif" } resolution = 3.8 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= 0.001 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 2 5.49 5 S 79 5.16 5 C 9865 2.51 5 N 2700 2.21 5 O 2894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15540 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3938 Classifications: {'peptide': 492} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 27, 'TRANS': 459} Chain: "B" Number of atoms: 3938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3938 Classifications: {'peptide': 492} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 27, 'TRANS': 458} Chain: "E" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3816 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 4, 'PTRANS': 22, 'TRANS': 452} Chain: "F" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3833 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 458} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'H6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.94, per 1000 atoms: 0.25 Number of scatterers: 15540 At special positions: 0 Unit cell: (96.743, 178.268, 258.706, 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 79 16.00 P 2 15.00 O 2894 8.00 N 2700 7.00 C 9865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 125 " distance=2.04 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 219 " distance=2.04 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 125 " distance=2.04 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 220 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 715.1 milliseconds 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 26 sheets defined 19.3% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 250 through 322 removed outlier: 3.518A pdb=" N ILE A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Proline residue: A 261 - end of helix removed outlier: 3.850A pdb=" N TRP A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.860A pdb=" N ARG B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.742A pdb=" N GLU B 119 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN B 120 " --> pdb=" O ALA B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 120' Processing helix chain 'B' and resid 250 through 321 removed outlier: 3.548A pdb=" N ILE B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Proline residue: B 261 - end of helix removed outlier: 3.631A pdb=" N ILE B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TRP B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 245 through 322 removed outlier: 4.412A pdb=" N ILE E 249 " --> pdb=" O ALA E 245 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Proline residue: E 257 - end of helix removed outlier: 3.661A pdb=" N ARG E 322 " --> pdb=" O GLN E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 337 removed outlier: 4.697A pdb=" N MET E 334 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 349 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 102 through 107 removed outlier: 4.245A pdb=" N THR F 105 " --> pdb=" O ASP F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 244 through 319 removed outlier: 3.505A pdb=" N TRP F 248 " --> pdb=" O SER F 244 " (cutoff:3.500A) Proline residue: F 257 - end of helix removed outlier: 3.816A pdb=" N ARG F 313 " --> pdb=" O LEU F 309 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TRP F 314 " --> pdb=" O GLU F 310 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE F 317 " --> pdb=" O ARG F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 337 Processing helix chain 'F' and resid 425 through 428 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.195A pdb=" N ILE A 39 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP A 134 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 127 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 153 removed outlier: 5.191A pdb=" N GLU A 164 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A 207 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE A 166 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR A 205 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG A 168 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 203 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 179 Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 179 Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 343 removed outlier: 4.529A pdb=" N LEU A 325 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU B 325 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 461 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR B 474 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE B 463 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 341 through 343 removed outlier: 3.643A pdb=" N PHE B 498 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU B 325 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU A 325 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 461 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR A 474 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE A 463 " --> pdb=" O ILE A 472 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 376 removed outlier: 3.624A pdb=" N TRP A 398 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 31 through 33 Processing sheet with id=AB1, first strand: chain 'B' and resid 39 through 42 Processing sheet with id=AB2, first strand: chain 'B' and resid 150 through 153 removed outlier: 5.420A pdb=" N GLU B 164 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL B 207 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE B 166 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR B 205 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ARG B 168 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 203 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS B 190 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 185 through 186 removed outlier: 4.596A pdb=" N TRP B 178 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 218 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B 232 " --> pdb=" O CYS B 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 374 through 375 removed outlier: 4.144A pdb=" N TRP B 398 " --> pdb=" O MET B 426 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR B 431 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 40 through 43 removed outlier: 6.222A pdb=" N SER E 69 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL E 75 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 50 through 53 removed outlier: 4.102A pdb=" N ALA E 110 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 190 through 191 removed outlier: 3.818A pdb=" N VAL E 195 " --> pdb=" O ALA E 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 190 through 191 removed outlier: 6.638A pdb=" N VAL E 204 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THR E 169 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ALA E 206 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ARG E 167 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL E 208 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU E 165 " --> pdb=" O VAL E 208 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N MET E 210 " --> pdb=" O HIS E 163 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N HIS E 163 " --> pdb=" O MET E 210 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY E 156 " --> pdb=" O HIS E 163 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU E 165 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL E 154 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG E 167 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE E 152 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TRP F 179 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.597A pdb=" N TRP E 179 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N VAL F 152 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER E 234 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL F 154 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER E 236 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLY F 156 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL F 152 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG F 167 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL F 154 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLU F 165 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY F 156 " --> pdb=" O HIS F 163 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS F 163 " --> pdb=" O MET F 210 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET F 210 " --> pdb=" O HIS F 163 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLU F 165 " --> pdb=" O VAL F 208 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL F 208 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ARG F 167 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA F 206 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR F 169 " --> pdb=" O VAL F 204 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL F 204 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 353 through 355 Processing sheet with id=AC2, first strand: chain 'E' and resid 397 through 400 removed outlier: 5.610A pdb=" N ASN E 476 " --> pdb=" O HIS E 482 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS E 482 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 450 through 452 removed outlier: 4.195A pdb=" N THR E 450 " --> pdb=" O ALA E 444 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 444 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR E 442 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 40 through 42 removed outlier: 6.092A pdb=" N ILE F 40 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP F 67 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN F 74 " --> pdb=" O SER F 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 48 through 51 Processing sheet with id=AC6, first strand: chain 'F' and resid 353 through 355 Processing sheet with id=AC7, first strand: chain 'F' and resid 383 through 385 removed outlier: 3.562A pdb=" N THR F 449 " --> pdb=" O THR F 443 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 481 through 485 removed outlier: 5.750A pdb=" N HIS F 481 " --> pdb=" O ASN F 475 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASN F 475 " --> pdb=" O HIS F 481 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR F 509 " --> pdb=" O GLU F 400 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1671 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: 3.07 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5131 1.34 - 1.46: 3222 1.46 - 1.58: 7435 1.58 - 1.70: 3 1.70 - 1.81: 117 Bond restraints: 15908 Sorted by residual: bond pdb=" O16 H6P F 601 " pdb=" P17 H6P F 601 " ideal model delta sigma weight residual 1.697 1.645 0.052 2.00e-02 2.50e+03 6.86e+00 bond pdb=" O16 H6P F 601 " pdb=" P13 H6P F 601 " ideal model delta sigma weight residual 1.594 1.646 -0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" C28 H6P F 601 " pdb=" O29 H6P F 601 " ideal model delta sigma weight residual 1.442 1.397 0.045 2.00e-02 2.50e+03 5.06e+00 bond pdb=" C31 H6P F 601 " pdb=" O33 H6P F 601 " ideal model delta sigma weight residual 1.440 1.398 0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" C27 H6P F 601 " pdb=" C28 H6P F 601 " ideal model delta sigma weight residual 1.495 1.528 -0.033 2.00e-02 2.50e+03 2.69e+00 ... (remaining 15903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 21324 2.26 - 4.52: 218 4.52 - 6.78: 15 6.78 - 9.04: 2 9.04 - 11.30: 2 Bond angle restraints: 21561 Sorted by residual: angle pdb=" C LYS E 325 " pdb=" N SER E 326 " pdb=" CA SER E 326 " ideal model delta sigma weight residual 121.70 129.02 -7.32 1.80e+00 3.09e-01 1.65e+01 angle pdb=" P13 H6P F 601 " pdb=" O16 H6P F 601 " pdb=" P17 H6P F 601 " ideal model delta sigma weight residual 135.28 123.98 11.30 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C LYS E 183 " pdb=" N GLY E 184 " pdb=" CA GLY E 184 " ideal model delta sigma weight residual 121.70 127.94 -6.24 1.80e+00 3.09e-01 1.20e+01 angle pdb=" O14 H6P F 601 " pdb=" P13 H6P F 601 " pdb=" O15 H6P F 601 " ideal model delta sigma weight residual 118.65 108.50 10.15 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C VAL A 244 " pdb=" N SER A 245 " pdb=" CA SER A 245 " ideal model delta sigma weight residual 121.70 127.19 -5.49 1.80e+00 3.09e-01 9.30e+00 ... (remaining 21556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8372 17.98 - 35.95: 975 35.95 - 53.93: 207 53.93 - 71.91: 52 71.91 - 89.88: 26 Dihedral angle restraints: 9632 sinusoidal: 3999 harmonic: 5633 Sorted by residual: dihedral pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual 93.00 29.58 63.42 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS F 166 " pdb=" SG CYS F 166 " pdb=" SG CYS F 220 " pdb=" CB CYS F 220 " ideal model delta sinusoidal sigma weight residual 93.00 48.39 44.61 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CA PHE E 486 " pdb=" C PHE E 486 " pdb=" N PRO E 487 " pdb=" CA PRO E 487 " ideal model delta harmonic sigma weight residual -180.00 -155.63 -24.37 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 9629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1409 0.031 - 0.062: 598 0.062 - 0.094: 158 0.094 - 0.125: 157 0.125 - 0.156: 17 Chirality restraints: 2339 Sorted by residual: chirality pdb=" CA VAL E 411 " pdb=" N VAL E 411 " pdb=" C VAL E 411 " pdb=" CB VAL E 411 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA ILE A 440 " pdb=" N ILE A 440 " pdb=" C ILE A 440 " pdb=" CB ILE A 440 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE F 471 " pdb=" N ILE F 471 " pdb=" C ILE F 471 " pdb=" CB ILE F 471 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 2336 not shown) Planarity restraints: 2795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 365 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO A 366 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 366 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 366 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 50 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO F 51 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO F 51 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 51 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 482 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO B 483 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 483 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 483 " 0.027 5.00e-02 4.00e+02 ... (remaining 2792 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 174 2.60 - 3.18: 13322 3.18 - 3.75: 22838 3.75 - 4.33: 31976 4.33 - 4.90: 54924 Nonbonded interactions: 123234 Sorted by model distance: nonbonded pdb=" OG SER F 356 " pdb=" OD1 ASP F 358 " model vdw 2.031 3.040 nonbonded pdb=" NZ LYS B 79 " pdb=" OE2 GLU E 135 " model vdw 2.068 3.120 nonbonded pdb=" NH2 ARG A 469 " pdb=" O PRO B 501 " model vdw 2.086 3.120 nonbonded pdb=" OD2 ASP F 153 " pdb=" NE ARG F 167 " model vdw 2.092 3.120 nonbonded pdb=" O LEU A 341 " pdb=" NH2 ARG A 356 " model vdw 2.104 3.120 ... (remaining 123229 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'E' and (resid 30 through 65 or resid 67 through 151 or resid 154 through \ 157 or resid 159 through 177 or resid 179 through 180 or resid 183 through 188 \ or resid 190 through 215 or resid 217 through 220 or resid 222 through 223 or re \ sid 225 through 246 or resid 248 through 257 or resid 260 through 263 or resid 2 \ 65 through 266 or resid 268 through 271 or resid 273 through 274 or resid 276 th \ rough 277 or resid 282 or resid 286 through 287 or resid 289 or resid 292 throug \ h 293 or resid 300 through 301 or resid 303 or resid 305 or resid 307 through 30 \ 8 or resid 310 through 312 or resid 314 through 315 or resid 317 through 319 or \ resid 322 through 324 or resid 328 through 329 or resid 331 through 333 or resid \ 335 through 346 or resid 348 through 350 or resid 352 through 365 or resid 367 \ through 368 or resid 370 through 378 or resid 380 or resid 382 through 388 or re \ sid 390 or resid 392 through 416 or resid 418 through 419 or resid 421 through 4 \ 30 or resid 432 through 443 or resid 445 through 455 or resid 457 through 458 or \ resid 460 through 462 or resid 464 through 470 or resid 472 through 477 or resi \ d 479 through 483 or resid 485 through 486 or resid 490 through 493 or resid 495 \ through 510 or (resid 511 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)))) selection = (chain 'F' and (resid 30 through 65 or resid 67 through 151 or resid 154 through \ 157 or resid 159 through 177 or resid 179 through 180 or resid 183 through 188 \ or resid 190 through 215 or resid 217 through 220 or resid 222 through 223 or re \ sid 225 through 246 or resid 248 through 257 or resid 260 through 263 or resid 2 \ 65 through 266 or resid 268 through 271 or resid 273 through 274 or resid 276 th \ rough 277 or resid 282 or resid 286 through 287 or resid 289 or resid 292 throug \ h 293 or resid 300 through 301 or resid 303 or resid 305 or resid 307 through 30 \ 8 or resid 310 through 312 or resid 314 through 315 or resid 317 through 319 or \ resid 322 through 324 or resid 328 through 329 or resid 331 through 333 or resid \ 335 through 346 or resid 348 through 350 or resid 352 through 365 or resid 367 \ through 368 or resid 370 through 378 or resid 380 or resid 382 through 388 or re \ sid 390 or resid 392 through 416 or resid 418 through 429 or resid 431 through 4 \ 42 or resid 444 through 454 or resid 456 through 457 or resid 459 through 461 or \ resid 463 through 469 or resid 471 through 476 or resid 478 through 482 or resi \ d 484 through 485 or resid 489 through 492 or resid 494 through 510)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.800 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.400 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 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 0.052 15918 Z= 0.166 Angle : 0.589 11.301 21581 Z= 0.311 Chirality : 0.044 0.156 2339 Planarity : 0.004 0.052 2795 Dihedral : 16.656 89.882 5978 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.18 % Allowed : 18.39 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.71 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.19), residues: 1942 helix: 2.76 (0.27), residues: 312 sheet: -0.91 (0.21), residues: 583 loop : -1.50 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 351 TYR 0.013 0.001 TYR F 396 PHE 0.012 0.001 PHE E 474 TRP 0.015 0.001 TRP F 332 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (15908) covalent geometry : angle 0.58874 / 0.31 (21561) SS BOND : bond 0.00379 / 0.20 ( 10) SS BOND : angle 1.04523 / 0.60 ( 20) hydrogen bonds : bond 0.12831 / 8.56 ( 619) hydrogen bonds : angle 6.46587 / 4.48 ( 1671) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 137 average time/residue: 0.1473 time to fit residues: 29.3736 Evaluate side-chains 65 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN E 415 ASN F 163 HIS F 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.084214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.062325 restraints weight = 81924.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.063843 restraints weight = 49433.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.064153 restraints weight = 31988.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.064549 restraints weight = 28419.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.064463 restraints weight = 25677.204| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15918 Z= 0.190 Angle : 0.653 8.316 21581 Z= 0.339 Chirality : 0.046 0.179 2339 Planarity : 0.005 0.047 2795 Dihedral : 5.220 66.316 2164 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.07 % Allowed : 18.98 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.71 % Cis-general : 0.44 % 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: -0.57 (0.19), residues: 1942 helix: 3.25 (0.27), residues: 315 sheet: -0.86 (0.20), residues: 607 loop : -1.26 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 520 TYR 0.012 0.001 TYR B 126 PHE 0.024 0.002 PHE A 71 TRP 0.022 0.002 TRP F 332 HIS 0.006 0.001 HIS F 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (15908) covalent geometry : angle 0.65100 / 0.34 (21561) SS BOND : bond 0.00808 / 0.39 ( 10) SS BOND : angle 1.85068 / 1.04 ( 20) hydrogen bonds : bond 0.05724 / 3.78 ( 619) hydrogen bonds : angle 5.34375 / 3.68 ( 1671) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 GLU cc_start: 0.8721 (mp0) cc_final: 0.8514 (tm-30) REVERT: A 399 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.7248 (t) REVERT: A 490 LEU cc_start: 0.9061 (tp) cc_final: 0.8786 (tp) REVERT: B 62 MET cc_start: 0.8749 (mtt) cc_final: 0.8435 (mtt) REVERT: B 209 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7246 (tt) REVERT: B 217 MET cc_start: 0.6778 (ttm) cc_final: 0.6547 (ttm) REVERT: B 365 ASN cc_start: 0.9383 (OUTLIER) cc_final: 0.9160 (p0) REVERT: E 63 MET cc_start: 0.8669 (mmm) cc_final: 0.8352 (mmm) REVERT: E 434 MET cc_start: 0.7740 (tpt) cc_final: 0.7117 (tmm) REVERT: F 58 MET cc_start: 0.4229 (pmm) cc_final: 0.3846 (pmm) REVERT: F 63 MET cc_start: 0.5454 (mmm) cc_final: 0.5033 (mmm) REVERT: F 93 TYR cc_start: 0.6616 (m-80) cc_final: 0.5695 (m-80) REVERT: F 293 MET cc_start: 0.8223 (ppp) cc_final: 0.8014 (ppp) outliers start: 35 outliers final: 10 residues processed: 107 average time/residue: 0.1385 time to fit residues: 22.0904 Evaluate side-chains 75 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain F residue 136 LYS Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 510 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 178 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.0050 chunk 101 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN F 280 GLN F 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.083237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.061592 restraints weight = 79019.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.063069 restraints weight = 46623.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.063515 restraints weight = 30264.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.063733 restraints weight = 26301.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.063715 restraints weight = 23966.013| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15918 Z= 0.167 Angle : 0.608 11.329 21581 Z= 0.313 Chirality : 0.044 0.146 2339 Planarity : 0.004 0.045 2795 Dihedral : 5.050 67.549 2164 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.60 % Allowed : 19.28 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.71 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1942 helix: 3.08 (0.27), residues: 330 sheet: -0.79 (0.20), residues: 621 loop : -1.09 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 301 TYR 0.011 0.001 TYR A 387 PHE 0.018 0.001 PHE F 31 TRP 0.019 0.001 TRP F 332 HIS 0.020 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (15908) covalent geometry : angle 0.60607 / 0.31 (21561) SS BOND : bond 0.00792 / 0.40 ( 10) SS BOND : angle 1.68053 / 0.95 ( 20) hydrogen bonds : bond 0.05495 / 3.66 ( 619) hydrogen bonds : angle 5.17342 / 3.56 ( 1671) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 THR cc_start: 0.7560 (OUTLIER) cc_final: 0.7349 (t) REVERT: A 426 MET cc_start: 0.7706 (mmm) cc_final: 0.7175 (mmm) REVERT: A 490 LEU cc_start: 0.9080 (tp) cc_final: 0.8846 (tp) REVERT: B 62 MET cc_start: 0.8759 (mtt) cc_final: 0.8558 (mtt) REVERT: B 196 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7060 (p0) REVERT: B 209 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7687 (tt) REVERT: E 58 MET cc_start: 0.8786 (ppp) cc_final: 0.8503 (ppp) REVERT: E 63 MET cc_start: 0.8681 (mmm) cc_final: 0.8305 (mmm) REVERT: E 425 MET cc_start: 0.4671 (ttt) cc_final: 0.4022 (mtm) REVERT: E 434 MET cc_start: 0.7585 (tpt) cc_final: 0.6953 (tmm) REVERT: F 58 MET cc_start: 0.4187 (pmm) cc_final: 0.3642 (pmm) REVERT: F 63 MET cc_start: 0.5641 (mmm) cc_final: 0.5272 (mmm) outliers start: 27 outliers final: 13 residues processed: 92 average time/residue: 0.1338 time to fit residues: 19.1059 Evaluate side-chains 78 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 510 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 142 optimal weight: 50.0000 chunk 95 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN ** F 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.080162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.058002 restraints weight = 81602.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.059214 restraints weight = 51310.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.059406 restraints weight = 35978.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.059833 restraints weight = 31922.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.059718 restraints weight = 28678.198| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 15918 Z= 0.307 Angle : 0.715 8.480 21581 Z= 0.374 Chirality : 0.046 0.160 2339 Planarity : 0.005 0.052 2795 Dihedral : 5.644 62.581 2164 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.96 % Allowed : 19.04 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.71 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.76 (0.19), residues: 1942 helix: 2.48 (0.27), residues: 334 sheet: -0.96 (0.20), residues: 612 loop : -1.23 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 321 TYR 0.020 0.002 TYR E 127 PHE 0.032 0.002 PHE B 201 TRP 0.026 0.002 TRP F 380 HIS 0.009 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.31 (15908) covalent geometry : angle 0.71176 / 0.37 (21561) SS BOND : bond 0.01077 / 0.53 ( 10) SS BOND : angle 2.37403 / 1.39 ( 20) hydrogen bonds : bond 0.05990 / 3.97 ( 619) hydrogen bonds : angle 5.61041 / 3.85 ( 1671) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 65 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8553 (p90) cc_final: 0.8037 (p90) REVERT: A 399 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7656 (t) REVERT: A 426 MET cc_start: 0.7449 (mmm) cc_final: 0.7186 (mmm) REVERT: A 490 LEU cc_start: 0.9346 (tp) cc_final: 0.9084 (tp) REVERT: B 62 MET cc_start: 0.8952 (mtt) cc_final: 0.8719 (mtt) REVERT: B 194 MET cc_start: 0.7840 (ppp) cc_final: 0.7574 (ppp) REVERT: B 196 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7240 (p0) REVERT: B 202 MET cc_start: 0.8085 (ppp) cc_final: 0.7524 (ppp) REVERT: B 209 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7916 (tt) REVERT: B 454 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8320 (tp) REVERT: E 58 MET cc_start: 0.8791 (ppp) cc_final: 0.8503 (ppp) REVERT: E 63 MET cc_start: 0.8790 (mmm) cc_final: 0.8370 (mmt) REVERT: E 130 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7554 (t0) REVERT: E 425 MET cc_start: 0.4819 (ttt) cc_final: 0.3973 (mmp) REVERT: E 433 THR cc_start: 0.5235 (OUTLIER) cc_final: 0.4216 (p) REVERT: E 434 MET cc_start: 0.7787 (tpt) cc_final: 0.7555 (tpt) REVERT: F 58 MET cc_start: 0.4437 (pmm) cc_final: 0.3831 (pmm) REVERT: F 63 MET cc_start: 0.5645 (mmm) cc_final: 0.5309 (mmm) outliers start: 50 outliers final: 24 residues processed: 112 average time/residue: 0.1247 time to fit residues: 21.6509 Evaluate side-chains 90 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 332 TRP Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 219 SER Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain F residue 510 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 33 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 188 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 132 optimal weight: 30.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN F 326 HIS F 330 ASN F 408 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.081208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.059436 restraints weight = 81215.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.060667 restraints weight = 49416.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.061066 restraints weight = 33022.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.061313 restraints weight = 30269.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.061304 restraints weight = 27325.514| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15918 Z= 0.158 Angle : 0.582 9.393 21581 Z= 0.305 Chirality : 0.044 0.146 2339 Planarity : 0.004 0.046 2795 Dihedral : 5.232 66.673 2164 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.37 % Allowed : 19.52 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.71 % Cis-general : 0.44 % 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 (0.19), residues: 1942 helix: 2.92 (0.28), residues: 334 sheet: -0.76 (0.20), residues: 617 loop : -1.00 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 313 TYR 0.011 0.001 TYR E 127 PHE 0.014 0.001 PHE B 201 TRP 0.017 0.001 TRP F 380 HIS 0.004 0.001 HIS E 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (15908) covalent geometry : angle 0.58046 / 0.30 (21561) SS BOND : bond 0.00703 / 0.38 ( 10) SS BOND : angle 1.42101 / 0.82 ( 20) hydrogen bonds : bond 0.05452 / 3.63 ( 619) hydrogen bonds : angle 5.24326 / 3.61 ( 1671) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 62 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8519 (p90) cc_final: 0.7981 (p90) REVERT: A 173 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8637 (mmmm) REVERT: A 399 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7585 (t) REVERT: A 490 LEU cc_start: 0.9283 (tp) cc_final: 0.9031 (tp) REVERT: B 196 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7085 (p0) REVERT: B 209 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7792 (tt) REVERT: E 63 MET cc_start: 0.8604 (mmm) cc_final: 0.8307 (mmt) REVERT: E 425 MET cc_start: 0.4704 (ttt) cc_final: 0.3879 (mmp) REVERT: E 433 THR cc_start: 0.5013 (OUTLIER) cc_final: 0.4077 (p) REVERT: E 434 MET cc_start: 0.7674 (tpt) cc_final: 0.7464 (tpt) REVERT: F 33 VAL cc_start: 0.6335 (OUTLIER) cc_final: 0.5912 (m) REVERT: F 58 MET cc_start: 0.4629 (pmm) cc_final: 0.3940 (pmm) REVERT: F 63 MET cc_start: 0.5623 (mmm) cc_final: 0.5328 (mmm) outliers start: 40 outliers final: 21 residues processed: 101 average time/residue: 0.1120 time to fit residues: 18.0994 Evaluate side-chains 86 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 510 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 119 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN F 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.080113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.058291 restraints weight = 80897.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.059483 restraints weight = 50663.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059716 restraints weight = 34997.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.060081 restraints weight = 31390.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.059987 restraints weight = 27944.035| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15918 Z= 0.232 Angle : 0.629 9.680 21581 Z= 0.329 Chirality : 0.045 0.147 2339 Planarity : 0.004 0.050 2795 Dihedral : 5.394 61.886 2164 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.13 % Allowed : 19.57 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.71 % Cis-general : 0.44 % 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: -0.41 (0.19), residues: 1942 helix: 2.82 (0.28), residues: 334 sheet: -0.68 (0.20), residues: 613 loop : -1.07 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 291 TYR 0.014 0.002 TYR E 127 PHE 0.027 0.002 PHE A 71 TRP 0.021 0.002 TRP F 380 HIS 0.005 0.001 HIS F 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (15908) covalent geometry : angle 0.62682 / 0.33 (21561) SS BOND : bond 0.00867 / 0.44 ( 10) SS BOND : angle 1.81156 / 1.06 ( 20) hydrogen bonds : bond 0.05604 / 3.75 ( 619) hydrogen bonds : angle 5.38036 / 3.70 ( 1671) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 61 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8584 (p90) cc_final: 0.8047 (p90) REVERT: A 173 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8990 (tptp) REVERT: A 399 THR cc_start: 0.7846 (OUTLIER) cc_final: 0.7632 (t) REVERT: A 490 LEU cc_start: 0.9270 (tp) cc_final: 0.9044 (tp) REVERT: B 209 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7868 (tt) REVERT: E 63 MET cc_start: 0.8623 (mmm) cc_final: 0.8314 (mmt) REVERT: E 425 MET cc_start: 0.4546 (ttt) cc_final: 0.3963 (mtm) REVERT: E 433 THR cc_start: 0.5067 (OUTLIER) cc_final: 0.4455 (p) REVERT: E 434 MET cc_start: 0.7801 (tpt) cc_final: 0.6897 (tmm) REVERT: F 58 MET cc_start: 0.4526 (pmm) cc_final: 0.3785 (pmm) REVERT: F 63 MET cc_start: 0.5889 (mmm) cc_final: 0.5604 (mmm) outliers start: 53 outliers final: 34 residues processed: 110 average time/residue: 0.1139 time to fit residues: 19.8917 Evaluate side-chains 97 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 332 TRP Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 510 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 102 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 HIS ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN E 476 ASN F 326 HIS F 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.080822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.059333 restraints weight = 78740.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.060902 restraints weight = 46664.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061157 restraints weight = 29516.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.061422 restraints weight = 26497.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061369 restraints weight = 23933.889| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15918 Z= 0.147 Angle : 0.588 10.206 21581 Z= 0.305 Chirality : 0.044 0.157 2339 Planarity : 0.004 0.045 2795 Dihedral : 5.193 65.371 2164 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.66 % Allowed : 20.11 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.71 % Cis-general : 0.44 % 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: -0.15 (0.19), residues: 1942 helix: 3.20 (0.28), residues: 328 sheet: -0.57 (0.21), residues: 615 loop : -0.90 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 167 TYR 0.012 0.001 TYR B 267 PHE 0.011 0.001 PHE A 98 TRP 0.018 0.001 TRP B 268 HIS 0.003 0.001 HIS E 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (15908) covalent geometry : angle 0.58658 / 0.30 (21561) SS BOND : bond 0.00649 / 0.35 ( 10) SS BOND : angle 1.29904 / 0.76 ( 20) hydrogen bonds : bond 0.05297 / 3.54 ( 619) hydrogen bonds : angle 5.16293 / 3.57 ( 1671) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 57 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8600 (p90) cc_final: 0.8078 (p90) REVERT: A 399 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7602 (t) REVERT: A 490 LEU cc_start: 0.9213 (tp) cc_final: 0.8981 (tp) REVERT: B 209 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7864 (tt) REVERT: E 63 MET cc_start: 0.8602 (mmm) cc_final: 0.8269 (mmt) REVERT: E 425 MET cc_start: 0.4579 (ttt) cc_final: 0.3954 (mtm) REVERT: E 433 THR cc_start: 0.4946 (OUTLIER) cc_final: 0.4144 (p) REVERT: E 493 GLU cc_start: 0.1516 (OUTLIER) cc_final: 0.1094 (pm20) REVERT: F 58 MET cc_start: 0.4732 (pmm) cc_final: 0.4006 (pmm) REVERT: F 63 MET cc_start: 0.6010 (mmm) cc_final: 0.5732 (mmm) REVERT: F 325 ARG cc_start: 0.6008 (OUTLIER) cc_final: 0.5790 (mtm-85) outliers start: 45 outliers final: 29 residues processed: 100 average time/residue: 0.1109 time to fit residues: 17.8947 Evaluate side-chains 90 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 56 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 332 TRP Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 476 ASN Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 510 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 140 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 131 optimal weight: 50.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN E 476 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.080355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.058921 restraints weight = 79541.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060431 restraints weight = 46999.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.060751 restraints weight = 29705.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.060971 restraints weight = 26425.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060937 restraints weight = 24168.953| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15918 Z= 0.170 Angle : 0.600 10.480 21581 Z= 0.311 Chirality : 0.044 0.150 2339 Planarity : 0.004 0.047 2795 Dihedral : 5.164 63.249 2164 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.54 % Allowed : 20.05 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.71 % Cis-general : 0.44 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 1942 helix: 3.21 (0.28), residues: 328 sheet: -0.52 (0.21), residues: 607 loop : -0.87 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 291 TYR 0.012 0.001 TYR B 267 PHE 0.020 0.001 PHE A 71 TRP 0.019 0.001 TRP B 268 HIS 0.006 0.001 HIS E 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (15908) covalent geometry : angle 0.59859 / 0.31 (21561) SS BOND : bond 0.00697 / 0.36 ( 10) SS BOND : angle 1.41749 / 0.83 ( 20) hydrogen bonds : bond 0.05278 / 3.54 ( 619) hydrogen bonds : angle 5.16592 / 3.57 ( 1671) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 57 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8513 (p90) cc_final: 0.7968 (p90) REVERT: A 399 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7615 (t) REVERT: A 490 LEU cc_start: 0.9271 (tp) cc_final: 0.9048 (tp) REVERT: B 209 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.7963 (tt) REVERT: E 63 MET cc_start: 0.8613 (mmm) cc_final: 0.8289 (mmt) REVERT: E 425 MET cc_start: 0.4602 (ttt) cc_final: 0.3973 (mtm) REVERT: E 433 THR cc_start: 0.4767 (OUTLIER) cc_final: 0.4270 (p) REVERT: E 434 MET cc_start: 0.7742 (tpt) cc_final: 0.6882 (tmm) REVERT: E 493 GLU cc_start: 0.1470 (OUTLIER) cc_final: 0.1051 (pm20) REVERT: F 58 MET cc_start: 0.4929 (pmm) cc_final: 0.4177 (pmm) REVERT: F 63 MET cc_start: 0.5969 (mmm) cc_final: 0.5680 (mmm) outliers start: 43 outliers final: 32 residues processed: 97 average time/residue: 0.1095 time to fit residues: 17.2589 Evaluate side-chains 93 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 57 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 332 TRP Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 510 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 186 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN F 326 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.081535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.059967 restraints weight = 81443.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061171 restraints weight = 49913.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.061562 restraints weight = 33420.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.061853 restraints weight = 29386.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.061792 restraints weight = 26489.730| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15918 Z= 0.120 Angle : 0.584 11.375 21581 Z= 0.299 Chirality : 0.044 0.144 2339 Planarity : 0.004 0.045 2795 Dihedral : 4.942 64.474 2164 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.95 % Allowed : 20.76 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.71 % Cis-general : 0.44 % 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: 0.16 (0.20), residues: 1942 helix: 3.79 (0.27), residues: 315 sheet: -0.37 (0.21), residues: 612 loop : -0.77 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 167 TYR 0.011 0.001 TYR E 475 PHE 0.012 0.001 PHE A 98 TRP 0.018 0.001 TRP B 268 HIS 0.016 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (15908) covalent geometry : angle 0.58348 / 0.30 (21561) SS BOND : bond 0.00515 / 0.27 ( 10) SS BOND : angle 0.93510 / 0.54 ( 20) hydrogen bonds : bond 0.04964 / 3.33 ( 619) hydrogen bonds : angle 4.95660 / 3.43 ( 1671) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8527 (p90) cc_final: 0.8003 (p90) REVERT: A 399 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7573 (t) REVERT: A 490 LEU cc_start: 0.9272 (tp) cc_final: 0.8988 (tp) REVERT: B 209 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7873 (tt) REVERT: E 63 MET cc_start: 0.8582 (mmm) cc_final: 0.8244 (mmt) REVERT: E 434 MET cc_start: 0.7688 (tpt) cc_final: 0.6873 (tmm) REVERT: E 493 GLU cc_start: 0.1747 (OUTLIER) cc_final: 0.1287 (pm20) REVERT: F 58 MET cc_start: 0.5045 (pmm) cc_final: 0.4305 (pmm) REVERT: F 63 MET cc_start: 0.5896 (mmm) cc_final: 0.5657 (mmm) REVERT: F 146 LEU cc_start: 0.8971 (tp) cc_final: 0.8568 (tt) REVERT: F 325 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.6022 (mtm-85) outliers start: 33 outliers final: 26 residues processed: 96 average time/residue: 0.1125 time to fit residues: 17.3272 Evaluate side-chains 90 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 332 TRP Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 325 ARG Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain F residue 510 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 25 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 134 optimal weight: 50.0000 chunk 184 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 139 optimal weight: 50.0000 chunk 23 optimal weight: 0.1980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN F 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.080853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.059190 restraints weight = 80896.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.060412 restraints weight = 50140.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.060601 restraints weight = 34247.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.060994 restraints weight = 30283.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060935 restraints weight = 26909.508| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15918 Z= 0.159 Angle : 0.600 11.080 21581 Z= 0.308 Chirality : 0.044 0.151 2339 Planarity : 0.004 0.051 2795 Dihedral : 4.947 63.342 2164 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.95 % Allowed : 20.93 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.71 % Cis-general : 0.44 % 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: 0.12 (0.19), residues: 1942 helix: 3.59 (0.27), residues: 320 sheet: -0.37 (0.21), residues: 615 loop : -0.77 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 291 TYR 0.014 0.001 TYR B 431 PHE 0.023 0.001 PHE A 71 TRP 0.019 0.001 TRP B 268 HIS 0.022 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (15908) covalent geometry : angle 0.59948 / 0.31 (21561) SS BOND : bond 0.00610 / 0.28 ( 10) SS BOND : angle 1.20136 / 0.72 ( 20) hydrogen bonds : bond 0.05023 / 3.38 ( 619) hydrogen bonds : angle 5.02546 / 3.47 ( 1671) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8542 (p90) cc_final: 0.8029 (p90) REVERT: A 490 LEU cc_start: 0.9248 (tp) cc_final: 0.8987 (tp) REVERT: B 209 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7916 (tt) REVERT: E 63 MET cc_start: 0.8612 (mmm) cc_final: 0.8277 (mmt) REVERT: E 434 MET cc_start: 0.7691 (tpt) cc_final: 0.6842 (tmm) REVERT: E 493 GLU cc_start: 0.1734 (OUTLIER) cc_final: 0.1296 (pm20) REVERT: F 58 MET cc_start: 0.5026 (pmm) cc_final: 0.4268 (pmm) REVERT: F 93 TYR cc_start: 0.6938 (m-80) cc_final: 0.5835 (m-80) outliers start: 33 outliers final: 28 residues processed: 91 average time/residue: 0.1065 time to fit residues: 15.6435 Evaluate side-chains 88 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 156 HIS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 332 TRP Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 412 CYS Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain F residue 510 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 3 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 158 optimal weight: 0.0070 chunk 84 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN F 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.081638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.060354 restraints weight = 78665.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.062081 restraints weight = 45739.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.062203 restraints weight = 29563.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.062342 restraints weight = 25704.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.062380 restraints weight = 23731.687| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15918 Z= 0.115 Angle : 0.588 11.206 21581 Z= 0.300 Chirality : 0.044 0.148 2339 Planarity : 0.004 0.050 2795 Dihedral : 4.805 63.889 2164 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.77 % Allowed : 21.23 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.71 % Cis-general : 0.44 % 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: 0.28 (0.20), residues: 1942 helix: 3.84 (0.27), residues: 315 sheet: -0.21 (0.21), residues: 610 loop : -0.74 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 50 TYR 0.014 0.001 TYR A 431 PHE 0.012 0.001 PHE A 98 TRP 0.017 0.001 TRP B 268 HIS 0.031 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (15908) covalent geometry : angle 0.58764 / 0.30 (21561) SS BOND : bond 0.00526 / 0.30 ( 10) SS BOND : angle 0.84353 / 0.50 ( 20) hydrogen bonds : bond 0.04825 / 3.24 ( 619) hydrogen bonds : angle 4.88371 / 3.38 ( 1671) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2893.93 seconds wall clock time: 50 minutes 50.18 seconds (3050.18 seconds total)