Starting phenix.real_space_refine on Sat Aug 23 01:50:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hf6_34714/08_2025/8hf6_34714.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hf6_34714/08_2025/8hf6_34714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hf6_34714/08_2025/8hf6_34714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hf6_34714/08_2025/8hf6_34714.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hf6_34714/08_2025/8hf6_34714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hf6_34714/08_2025/8hf6_34714.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 28 5.16 5 C 5732 2.51 5 N 1464 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8916 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "B" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.99, per 1000 atoms: 0.22 Number of scatterers: 8916 At special positions: 0 Unit cell: (83.226, 84.084, 138.996, 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 28 16.00 P 6 15.00 O 1686 8.00 N 1464 7.00 C 5732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 324.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 69.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 157 through 164 removed outlier: 3.923A pdb=" N LEU A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 195 removed outlier: 3.656A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 251 removed outlier: 4.075A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 4.028A pdb=" N PHE A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 258 " --> pdb=" O MET A 254 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.622A pdb=" N ARG A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 304 removed outlier: 4.270A pdb=" N ASP A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.517A pdb=" N PHE A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 325 removed outlier: 3.992A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 353 removed outlier: 3.704A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 362 through 416 removed outlier: 4.087A pdb=" N ARG A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 460 removed outlier: 3.731A pdb=" N VAL A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.616A pdb=" N ASN A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 464 Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.597A pdb=" N VAL A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 588 through 598 Processing helix chain 'A' and resid 623 through 638 removed outlier: 3.865A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 removed outlier: 3.697A pdb=" N ALA A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.716A pdb=" N GLU A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 678 through 683' Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 709 through 717 Processing helix chain 'B' and resid 157 through 164 removed outlier: 3.953A pdb=" N GLN B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 196 removed outlier: 3.634A pdb=" N TYR B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 250 removed outlier: 3.809A pdb=" N ILE B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 removed outlier: 4.202A pdb=" N PHE B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 258 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 260' Processing helix chain 'B' and resid 261 through 276 removed outlier: 3.635A pdb=" N ILE B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 304 Processing helix chain 'B' and resid 305 through 312 removed outlier: 3.868A pdb=" N MET B 310 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 removed outlier: 4.064A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE B 325 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 352 removed outlier: 3.622A pdb=" N PHE B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU B 330 " --> pdb=" O MET B 326 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 362 through 417 removed outlier: 4.122A pdb=" N ARG B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 431 Processing helix chain 'B' and resid 431 through 460 Proline residue: B 437 - end of helix removed outlier: 4.196A pdb=" N THR B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 464 removed outlier: 3.646A pdb=" N VAL B 464 " --> pdb=" O VAL B 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 461 through 464' Processing helix chain 'B' and resid 522 through 531 removed outlier: 3.645A pdb=" N VAL B 531 " --> pdb=" O ALA B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 551 No H-bonds generated for 'chain 'B' and resid 549 through 551' Processing helix chain 'B' and resid 552 through 559 Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 588 through 598 removed outlier: 3.684A pdb=" N ALA B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 638 removed outlier: 3.752A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 666 removed outlier: 3.950A pdb=" N ALA B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 removed outlier: 4.593A pdb=" N ARG B 683 " --> pdb=" O THR B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.557A pdb=" N LEU B 704 " --> pdb=" O LYS B 700 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 717 Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.826A pdb=" N LEU A 500 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 489 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A 484 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 503 removed outlier: 3.826A pdb=" N LEU A 500 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 489 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 540 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL A 489 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN A 538 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 560 through 563 removed outlier: 6.367A pdb=" N ASN A 561 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP A 646 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 563 " --> pdb=" O ASP A 646 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 643 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE A 674 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU A 645 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 513 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS A 512 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL A 688 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA A 514 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU A 690 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 516 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 687 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU A 698 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A 689 " --> pdb=" O VAL A 696 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 506 through 507 removed outlier: 4.172A pdb=" N VAL B 489 " --> pdb=" O GLN B 538 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 538 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 546 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 560 through 563 removed outlier: 6.627A pdb=" N ASN B 561 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL B 513 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL B 688 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA B 514 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU B 690 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL B 516 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU B 697 " --> pdb=" O VAL B 689 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1466 1.29 - 1.42: 2144 1.42 - 1.55: 5371 1.55 - 1.68: 13 1.68 - 1.81: 56 Bond restraints: 9050 Sorted by residual: bond pdb=" CA ILE B 158 " pdb=" C ILE B 158 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.05e-02 9.07e+03 6.12e+01 bond pdb=" CA ILE B 286 " pdb=" C ILE B 286 " ideal model delta sigma weight residual 1.524 1.426 0.098 1.39e-02 5.18e+03 4.95e+01 bond pdb=" CA GLN A 647 " pdb=" CB GLN A 647 " ideal model delta sigma weight residual 1.530 1.427 0.103 1.48e-02 4.57e+03 4.87e+01 bond pdb=" CA SER A 156 " pdb=" C SER A 156 " ideal model delta sigma weight residual 1.523 1.431 0.092 1.34e-02 5.57e+03 4.70e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.58e+01 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 12051 3.37 - 6.75: 185 6.75 - 10.12: 29 10.12 - 13.50: 8 13.50 - 16.87: 5 Bond angle restraints: 12278 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 123.00 16.87 1.00e+00 1.00e+00 2.85e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 123.01 16.86 1.00e+00 1.00e+00 2.84e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 121.58 15.25 1.00e+00 1.00e+00 2.33e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 121.60 15.23 1.00e+00 1.00e+00 2.32e+02 angle pdb=" N SER A 156 " pdb=" CA SER A 156 " pdb=" C SER A 156 " ideal model delta sigma weight residual 112.88 99.00 13.88 1.29e+00 6.01e-01 1.16e+02 ... (remaining 12273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4901 17.91 - 35.82: 488 35.82 - 53.73: 91 53.73 - 71.64: 28 71.64 - 89.55: 10 Dihedral angle restraints: 5518 sinusoidal: 2224 harmonic: 3294 Sorted by residual: dihedral pdb=" C SER A 156 " pdb=" N SER A 156 " pdb=" CA SER A 156 " pdb=" CB SER A 156 " ideal model delta harmonic sigma weight residual -122.60 -104.93 -17.67 0 2.50e+00 1.60e-01 4.99e+01 dihedral pdb=" C TYR A 188 " pdb=" N TYR A 188 " pdb=" CA TYR A 188 " pdb=" CB TYR A 188 " ideal model delta harmonic sigma weight residual -122.60 -138.22 15.62 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" N TYR A 188 " pdb=" C TYR A 188 " pdb=" CA TYR A 188 " pdb=" CB TYR A 188 " ideal model delta harmonic sigma weight residual 122.80 136.78 -13.98 0 2.50e+00 1.60e-01 3.13e+01 ... (remaining 5515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1445 0.154 - 0.307: 45 0.307 - 0.461: 6 0.461 - 0.615: 1 0.615 - 0.768: 1 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CA TYR A 188 " pdb=" N TYR A 188 " pdb=" C TYR A 188 " pdb=" CB TYR A 188 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA THR B 361 " pdb=" N THR B 361 " pdb=" C THR B 361 " pdb=" CB THR B 361 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" CA ALA B 620 " pdb=" N ALA B 620 " pdb=" C ALA B 620 " pdb=" CB ALA B 620 " both_signs ideal model delta sigma weight residual False 2.48 2.05 0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 1495 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 647 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C GLN A 647 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN A 647 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 648 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 268 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.85e+00 pdb=" C ARG A 268 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG A 268 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE A 269 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 196 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.63e+00 pdb=" C TYR A 196 " -0.045 2.00e-02 2.50e+03 pdb=" O TYR A 196 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 197 " 0.015 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1308 2.75 - 3.28: 9189 3.28 - 3.82: 14266 3.82 - 4.36: 15970 4.36 - 4.90: 27576 Nonbonded interactions: 68309 Sorted by model distance: nonbonded pdb=" OD1 ASP A 653 " pdb=" OG1 THR A 656 " model vdw 2.207 3.040 nonbonded pdb=" N THR A 195 " pdb=" O THR A 195 " model vdw 2.282 2.496 nonbonded pdb=" OG1 THR B 524 " pdb=" O2G ATP B 801 " model vdw 2.288 3.040 nonbonded pdb=" O ALA B 640 " pdb=" NZ LYS B 669 " model vdw 2.290 3.120 nonbonded pdb=" N SER A 156 " pdb=" N PHE A 157 " model vdw 2.309 2.560 ... (remaining 68304 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.130 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 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 : 0.009 0.103 9050 Z= 0.645 Angle : 1.048 16.871 12278 Z= 0.713 Chirality : 0.067 0.768 1498 Planarity : 0.005 0.056 1522 Dihedral : 15.338 89.551 3394 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.63 % Favored : 95.10 % Rotamer: Outliers : 3.23 % Allowed : 2.83 % Favored : 93.94 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.26), residues: 1122 helix: 2.03 (0.20), residues: 698 sheet: 0.32 (0.66), residues: 66 loop : -1.70 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 593 TYR 0.016 0.001 TYR B 493 PHE 0.025 0.002 PHE A 269 TRP 0.011 0.002 TRP A 408 HIS 0.003 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00898 ( 9050) covalent geometry : angle 1.04771 (12278) hydrogen bonds : bond 0.19474 ( 534) hydrogen bonds : angle 5.37309 ( 1593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.352 Fit side-chains REVERT: A 201 MET cc_start: 0.8298 (ttm) cc_final: 0.8030 (ttm) REVERT: A 212 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8898 (mp) REVERT: B 678 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9145 (mt) outliers start: 32 outliers final: 15 residues processed: 129 average time/residue: 0.0848 time to fit residues: 15.6868 Evaluate side-chains 86 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 680 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 509 GLN A 676 HIS B 200 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN B 565 GLN B 663 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.101084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.078135 restraints weight = 19793.046| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.76 r_work: 0.3145 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9050 Z= 0.149 Angle : 0.560 9.814 12278 Z= 0.297 Chirality : 0.040 0.304 1498 Planarity : 0.003 0.037 1522 Dihedral : 8.892 88.280 1309 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.74 % Favored : 96.08 % Rotamer: Outliers : 2.02 % Allowed : 8.99 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.26), residues: 1122 helix: 2.53 (0.20), residues: 700 sheet: 0.50 (0.66), residues: 66 loop : -1.55 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 683 TYR 0.010 0.001 TYR B 187 PHE 0.012 0.001 PHE B 468 TRP 0.006 0.001 TRP A 408 HIS 0.010 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9050) covalent geometry : angle 0.56044 (12278) hydrogen bonds : bond 0.08004 ( 534) hydrogen bonds : angle 3.90737 ( 1593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.323 Fit side-chains REVERT: A 529 MET cc_start: 0.8783 (tpp) cc_final: 0.8524 (tpp) REVERT: B 298 LEU cc_start: 0.9259 (tp) cc_final: 0.8954 (tt) outliers start: 20 outliers final: 10 residues processed: 103 average time/residue: 0.0619 time to fit residues: 9.7989 Evaluate side-chains 85 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 713 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS B 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.095080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.071916 restraints weight = 20062.145| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.72 r_work: 0.3030 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9050 Z= 0.216 Angle : 0.615 10.045 12278 Z= 0.328 Chirality : 0.043 0.357 1498 Planarity : 0.003 0.030 1522 Dihedral : 7.577 79.937 1286 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.92 % Allowed : 12.53 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.26), residues: 1122 helix: 2.38 (0.20), residues: 704 sheet: 0.13 (0.64), residues: 66 loop : -1.69 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 683 TYR 0.013 0.001 TYR A 559 PHE 0.014 0.002 PHE B 468 TRP 0.005 0.001 TRP A 408 HIS 0.005 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 9050) covalent geometry : angle 0.61532 (12278) hydrogen bonds : bond 0.09360 ( 534) hydrogen bonds : angle 4.13829 ( 1593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 484 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8156 (mtp) outliers start: 19 outliers final: 14 residues processed: 89 average time/residue: 0.0760 time to fit residues: 9.9900 Evaluate side-chains 84 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 713 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS A 676 HIS ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.100384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.076784 restraints weight = 20004.631| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.82 r_work: 0.3101 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9050 Z= 0.135 Angle : 0.512 10.425 12278 Z= 0.269 Chirality : 0.039 0.272 1498 Planarity : 0.003 0.026 1522 Dihedral : 7.156 88.748 1286 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.92 % Allowed : 14.44 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.26), residues: 1122 helix: 2.72 (0.20), residues: 706 sheet: 0.23 (0.64), residues: 66 loop : -1.65 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 606 TYR 0.009 0.001 TYR B 228 PHE 0.010 0.001 PHE B 468 TRP 0.003 0.001 TRP A 408 HIS 0.008 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9050) covalent geometry : angle 0.51239 (12278) hydrogen bonds : bond 0.07279 ( 534) hydrogen bonds : angle 3.59291 ( 1593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 529 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7912 (mpp) REVERT: A 606 ARG cc_start: 0.8551 (mpp80) cc_final: 0.7883 (mpp80) REVERT: A 613 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8402 (m) REVERT: B 471 LYS cc_start: 0.8091 (mttt) cc_final: 0.7859 (mtpt) REVERT: B 480 MET cc_start: 0.8083 (mpp) cc_final: 0.7866 (mpp) outliers start: 19 outliers final: 8 residues processed: 95 average time/residue: 0.0676 time to fit residues: 9.6761 Evaluate side-chains 81 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 680 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 82 optimal weight: 0.2980 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS B 219 GLN ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.101424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.077887 restraints weight = 19723.435| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.81 r_work: 0.3126 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9050 Z= 0.128 Angle : 0.506 10.197 12278 Z= 0.262 Chirality : 0.038 0.217 1498 Planarity : 0.003 0.023 1522 Dihedral : 6.650 88.657 1284 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.12 % Allowed : 15.96 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.26), residues: 1122 helix: 2.86 (0.20), residues: 708 sheet: 0.33 (0.66), residues: 66 loop : -1.62 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 606 TYR 0.008 0.001 TYR B 228 PHE 0.016 0.001 PHE B 468 TRP 0.002 0.000 TRP A 408 HIS 0.006 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9050) covalent geometry : angle 0.50560 (12278) hydrogen bonds : bond 0.06750 ( 534) hydrogen bonds : angle 3.43085 ( 1593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 190 GLN cc_start: 0.7943 (tt0) cc_final: 0.7565 (tt0) REVERT: A 606 ARG cc_start: 0.8449 (mpp80) cc_final: 0.8183 (mpp80) REVERT: A 691 ASP cc_start: 0.8186 (t70) cc_final: 0.7674 (t0) REVERT: B 471 LYS cc_start: 0.8128 (mttt) cc_final: 0.7851 (mtpt) outliers start: 21 outliers final: 13 residues processed: 98 average time/residue: 0.0648 time to fit residues: 9.4379 Evaluate side-chains 87 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 713 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS ** B 663 ASN ** 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 = 0.3650 r_free = 0.3650 target = 0.102177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.078558 restraints weight = 19710.631| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.82 r_work: 0.3138 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9050 Z= 0.124 Angle : 0.512 10.109 12278 Z= 0.259 Chirality : 0.038 0.185 1498 Planarity : 0.003 0.023 1522 Dihedral : 6.529 89.185 1284 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.92 % Allowed : 16.57 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.27), residues: 1122 helix: 2.94 (0.20), residues: 708 sheet: 0.26 (0.65), residues: 66 loop : -1.59 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 683 TYR 0.008 0.001 TYR B 228 PHE 0.016 0.001 PHE A 710 TRP 0.004 0.001 TRP A 408 HIS 0.005 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9050) covalent geometry : angle 0.51184 (12278) hydrogen bonds : bond 0.06422 ( 534) hydrogen bonds : angle 3.31906 ( 1593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 529 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7840 (mpp) REVERT: A 606 ARG cc_start: 0.8502 (mpp80) cc_final: 0.8206 (mpp80) REVERT: B 480 MET cc_start: 0.8261 (mpp) cc_final: 0.8007 (mpp) outliers start: 19 outliers final: 15 residues processed: 97 average time/residue: 0.0774 time to fit residues: 11.1381 Evaluate side-chains 91 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 713 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 100 optimal weight: 0.0170 chunk 66 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 663 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.101583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077908 restraints weight = 19819.779| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.81 r_work: 0.3126 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9050 Z= 0.129 Angle : 0.521 10.544 12278 Z= 0.263 Chirality : 0.038 0.172 1498 Planarity : 0.003 0.023 1522 Dihedral : 6.444 87.539 1284 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.12 % Allowed : 16.46 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.27), residues: 1122 helix: 2.95 (0.20), residues: 708 sheet: 0.31 (0.66), residues: 66 loop : -1.59 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 601 TYR 0.008 0.001 TYR B 228 PHE 0.015 0.001 PHE A 710 TRP 0.004 0.001 TRP A 408 HIS 0.003 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9050) covalent geometry : angle 0.52131 (12278) hydrogen bonds : bond 0.06567 ( 534) hydrogen bonds : angle 3.32599 ( 1593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 529 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7840 (mpp) REVERT: A 606 ARG cc_start: 0.8426 (mpp80) cc_final: 0.8120 (mpp80) outliers start: 21 outliers final: 14 residues processed: 90 average time/residue: 0.0784 time to fit residues: 10.7097 Evaluate side-chains 86 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 713 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 84 optimal weight: 0.3980 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 663 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.098772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.075162 restraints weight = 19826.196| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.81 r_work: 0.3075 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9050 Z= 0.151 Angle : 0.544 11.282 12278 Z= 0.277 Chirality : 0.039 0.146 1498 Planarity : 0.003 0.022 1522 Dihedral : 6.472 86.042 1284 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.12 % Allowed : 17.07 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.26), residues: 1122 helix: 2.97 (0.20), residues: 698 sheet: 0.21 (0.65), residues: 66 loop : -1.67 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 601 TYR 0.009 0.001 TYR B 228 PHE 0.013 0.001 PHE A 710 TRP 0.004 0.001 TRP A 408 HIS 0.003 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9050) covalent geometry : angle 0.54370 (12278) hydrogen bonds : bond 0.07420 ( 534) hydrogen bonds : angle 3.50105 ( 1593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 529 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.7871 (mpp) REVERT: A 606 ARG cc_start: 0.8408 (mpp80) cc_final: 0.8055 (mpp80) REVERT: B 480 MET cc_start: 0.8299 (mpp) cc_final: 0.8051 (mpp) outliers start: 21 outliers final: 16 residues processed: 88 average time/residue: 0.0831 time to fit residues: 10.9089 Evaluate side-chains 89 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 713 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 32 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 0.0670 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.103529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.080073 restraints weight = 19539.626| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.81 r_work: 0.3161 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9050 Z= 0.123 Angle : 0.519 12.446 12278 Z= 0.260 Chirality : 0.038 0.150 1498 Planarity : 0.003 0.024 1522 Dihedral : 6.393 87.158 1284 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.52 % Allowed : 17.68 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.27), residues: 1122 helix: 2.88 (0.20), residues: 722 sheet: -0.05 (0.64), residues: 70 loop : -1.72 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 601 TYR 0.008 0.001 TYR B 228 PHE 0.013 0.001 PHE A 710 TRP 0.003 0.001 TRP B 408 HIS 0.002 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9050) covalent geometry : angle 0.51918 (12278) hydrogen bonds : bond 0.06061 ( 534) hydrogen bonds : angle 3.21954 ( 1593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 529 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7710 (mpp) REVERT: A 606 ARG cc_start: 0.8352 (mpp80) cc_final: 0.7932 (mpp80) REVERT: B 250 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.6982 (t80) REVERT: B 480 MET cc_start: 0.8265 (mpp) cc_final: 0.8025 (mpp) outliers start: 15 outliers final: 12 residues processed: 89 average time/residue: 0.0902 time to fit residues: 11.8236 Evaluate side-chains 90 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 713 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.102140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.078433 restraints weight = 19616.533| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.81 r_work: 0.3135 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9050 Z= 0.129 Angle : 0.548 12.562 12278 Z= 0.272 Chirality : 0.038 0.154 1498 Planarity : 0.003 0.023 1522 Dihedral : 6.346 86.338 1284 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.72 % Allowed : 17.68 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.27), residues: 1122 helix: 2.94 (0.20), residues: 710 sheet: -0.07 (0.64), residues: 70 loop : -1.65 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 601 TYR 0.012 0.001 TYR A 216 PHE 0.012 0.001 PHE A 710 TRP 0.002 0.001 TRP A 408 HIS 0.004 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9050) covalent geometry : angle 0.54755 (12278) hydrogen bonds : bond 0.06429 ( 534) hydrogen bonds : angle 3.28406 ( 1593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 529 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.7848 (mpp) REVERT: A 606 ARG cc_start: 0.8341 (mpp80) cc_final: 0.7901 (mpp80) REVERT: B 250 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7101 (t80) REVERT: B 298 LEU cc_start: 0.9281 (tt) cc_final: 0.9074 (tp) REVERT: B 480 MET cc_start: 0.8254 (mpp) cc_final: 0.8019 (mpp) REVERT: B 497 ARG cc_start: 0.6746 (tmm-80) cc_final: 0.6486 (tmm-80) outliers start: 17 outliers final: 13 residues processed: 91 average time/residue: 0.0956 time to fit residues: 12.5972 Evaluate side-chains 89 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 713 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.099683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075784 restraints weight = 19596.835| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.80 r_work: 0.3091 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9050 Z= 0.142 Angle : 0.554 12.663 12278 Z= 0.279 Chirality : 0.038 0.154 1498 Planarity : 0.003 0.030 1522 Dihedral : 6.339 85.471 1284 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.62 % Allowed : 18.48 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.26), residues: 1122 helix: 2.85 (0.20), residues: 710 sheet: -0.23 (0.63), residues: 70 loop : -1.70 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 601 TYR 0.015 0.001 TYR A 216 PHE 0.013 0.001 PHE A 710 TRP 0.004 0.001 TRP A 408 HIS 0.003 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9050) covalent geometry : angle 0.55410 (12278) hydrogen bonds : bond 0.07163 ( 534) hydrogen bonds : angle 3.42746 ( 1593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1770.83 seconds wall clock time: 31 minutes 8.26 seconds (1868.26 seconds total)