Starting phenix.real_space_refine on Thu Mar 13 16:31:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hf6_34714/03_2025/8hf6_34714.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hf6_34714/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hf6_34714/03_2025/8hf6_34714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hf6_34714/03_2025/8hf6_34714.map" model { file = "/net/cci-nas-00/data/ceres_data/8hf6_34714/03_2025/8hf6_34714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hf6_34714/03_2025/8hf6_34714.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.56, per 1000 atoms: 0.62 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: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.96 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: 2.59 Time building geometry restraints manager: 2.52 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: 0.04 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: 1.140 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.670 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.370 ------------------------------------------------------------------------------- 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= 0.573 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP A 408 HIS 0.003 0.001 HIS A 248 PHE 0.025 0.002 PHE A 269 TYR 0.016 0.001 TYR B 493 ARG 0.006 0.001 ARG A 593 *********************** 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 : 0.987 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: 0.1968 time to fit residues: 36.3799 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 : 1.046 ------------------------------------------------------------------------------- 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 94 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 676 HIS B 200 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.098050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074826 restraints weight = 19794.499| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.74 r_work: 0.3096 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9050 Z= 0.229 Angle : 0.586 9.755 12278 Z= 0.314 Chirality : 0.041 0.309 1498 Planarity : 0.003 0.038 1522 Dihedral : 9.100 85.070 1309 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.92 % Favored : 95.90 % Rotamer: Outliers : 2.42 % Allowed : 8.99 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.26), residues: 1122 helix: 2.41 (0.20), residues: 700 sheet: 0.34 (0.65), residues: 66 loop : -1.60 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 408 HIS 0.008 0.001 HIS A 676 PHE 0.013 0.001 PHE B 468 TYR 0.010 0.001 TYR B 228 ARG 0.005 0.000 ARG B 683 *********************** 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: 24 poor density : 82 time to evaluate : 0.954 Fit side-chains REVERT: A 409 MET cc_start: 0.7893 (mmp) cc_final: 0.7664 (tpp) REVERT: A 607 MET cc_start: 0.7758 (pmm) cc_final: 0.7369 (pmm) outliers start: 24 outliers final: 16 residues processed: 101 average time/residue: 0.1603 time to fit residues: 24.5847 Evaluate side-chains 89 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 204 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 275 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 249 VAL Chi-restraints excluded: chain B residue 297 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS A 509 GLN A 676 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.098805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.075827 restraints weight = 20124.598| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.75 r_work: 0.3105 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1729 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= 0.200 Angle : 0.537 10.198 12278 Z= 0.286 Chirality : 0.040 0.346 1498 Planarity : 0.003 0.028 1522 Dihedral : 7.751 75.854 1291 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.12 % Allowed : 11.62 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.26), residues: 1122 helix: 2.58 (0.20), residues: 702 sheet: 0.32 (0.65), residues: 66 loop : -1.61 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 408 HIS 0.004 0.001 HIS A 676 PHE 0.011 0.001 PHE B 468 TYR 0.016 0.001 TYR A 559 ARG 0.003 0.000 ARG B 683 *********************** 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 102 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 606 ARG cc_start: 0.8699 (mtm110) cc_final: 0.8096 (mpp80) REVERT: A 607 MET cc_start: 0.7938 (pmm) cc_final: 0.7668 (pmm) REVERT: B 298 LEU cc_start: 0.9284 (tp) cc_final: 0.8969 (tt) REVERT: B 471 LYS cc_start: 0.8082 (mttt) cc_final: 0.7811 (mtpt) outliers start: 21 outliers final: 14 residues processed: 95 average time/residue: 0.1722 time to fit residues: 24.6405 Evaluate side-chains 88 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 642 VAL 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 401 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 469 GLU 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 96 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.098597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.074918 restraints weight = 19832.037| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.80 r_work: 0.3070 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9050 Z= 0.205 Angle : 0.537 10.250 12278 Z= 0.283 Chirality : 0.040 0.346 1498 Planarity : 0.003 0.024 1522 Dihedral : 7.079 88.285 1286 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.02 % Allowed : 13.54 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.26), residues: 1122 helix: 2.68 (0.20), residues: 702 sheet: 0.19 (0.64), residues: 66 loop : -1.66 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 408 HIS 0.008 0.001 HIS A 676 PHE 0.011 0.001 PHE B 468 TYR 0.009 0.001 TYR B 228 ARG 0.003 0.000 ARG B 683 *********************** 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 95 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 607 MET cc_start: 0.7981 (pmm) cc_final: 0.7706 (pmm) REVERT: B 471 LYS cc_start: 0.8119 (mttt) cc_final: 0.7845 (mtpt) outliers start: 20 outliers final: 14 residues processed: 90 average time/residue: 0.1836 time to fit residues: 24.2785 Evaluate side-chains 85 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 212 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 642 VAL 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 412 VAL Chi-restraints excluded: chain B residue 469 GLU 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 29 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 105 optimal weight: 0.0030 chunk 104 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.104153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.080889 restraints weight = 19555.626| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.79 r_work: 0.3177 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9050 Z= 0.145 Angle : 0.493 10.395 12278 Z= 0.255 Chirality : 0.039 0.361 1498 Planarity : 0.003 0.024 1522 Dihedral : 6.778 89.809 1286 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.12 % Allowed : 14.75 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.27), residues: 1122 helix: 2.96 (0.20), residues: 708 sheet: 0.34 (0.66), residues: 66 loop : -1.61 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 408 HIS 0.011 0.001 HIS A 676 PHE 0.009 0.001 PHE B 468 TYR 0.008 0.001 TYR B 228 ARG 0.003 0.000 ARG A 606 *********************** 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 117 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 529 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7738 (mpp) REVERT: A 691 ASP cc_start: 0.8150 (t70) cc_final: 0.7646 (t0) REVERT: B 298 LEU cc_start: 0.9229 (tp) cc_final: 0.8954 (tt) REVERT: B 471 LYS cc_start: 0.8041 (mttt) cc_final: 0.7777 (mtpt) outliers start: 21 outliers final: 9 residues processed: 106 average time/residue: 0.2247 time to fit residues: 35.0163 Evaluate side-chains 88 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 642 VAL Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 469 GLU 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 24 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.100727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.077668 restraints weight = 19840.079| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.72 r_work: 0.3142 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9050 Z= 0.189 Angle : 0.534 10.280 12278 Z= 0.270 Chirality : 0.039 0.279 1498 Planarity : 0.003 0.022 1522 Dihedral : 6.498 86.675 1284 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.92 % Allowed : 16.36 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.26), residues: 1122 helix: 2.88 (0.20), residues: 708 sheet: 0.20 (0.65), residues: 66 loop : -1.58 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 408 HIS 0.005 0.001 HIS A 676 PHE 0.014 0.001 PHE A 710 TYR 0.009 0.001 TYR B 228 ARG 0.004 0.000 ARG A 606 *********************** 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 96 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 298 LEU cc_start: 0.9265 (tp) cc_final: 0.8946 (tt) REVERT: B 471 LYS cc_start: 0.8073 (mttt) cc_final: 0.7851 (mtpt) outliers start: 19 outliers final: 13 residues processed: 92 average time/residue: 0.2247 time to fit residues: 30.5363 Evaluate side-chains 84 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 397 VAL 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 297 SER Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 469 GLU 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 4 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** 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 = 0.3595 r_free = 0.3595 target = 0.098073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.074455 restraints weight = 20116.450| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.84 r_work: 0.3059 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9050 Z= 0.214 Angle : 0.548 10.561 12278 Z= 0.280 Chirality : 0.040 0.296 1498 Planarity : 0.003 0.040 1522 Dihedral : 6.511 84.838 1284 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.72 % Allowed : 16.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.26), residues: 1122 helix: 2.77 (0.20), residues: 710 sheet: 0.11 (0.64), residues: 66 loop : -1.66 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 408 HIS 0.003 0.001 HIS A 248 PHE 0.015 0.001 PHE A 710 TYR 0.010 0.001 TYR B 228 ARG 0.005 0.000 ARG A 606 *********************** 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 90 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: B 471 LYS cc_start: 0.8116 (mttt) cc_final: 0.7846 (mtpt) REVERT: B 662 ASP cc_start: 0.8180 (m-30) cc_final: 0.7957 (m-30) outliers start: 17 outliers final: 14 residues processed: 86 average time/residue: 0.1928 time to fit residues: 25.7770 Evaluate side-chains 85 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 397 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.0030 chunk 96 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 ASN ** 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 = 0.3669 r_free = 0.3669 target = 0.103566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.080442 restraints weight = 20071.966| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.83 r_work: 0.3169 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9050 Z= 0.142 Angle : 0.527 11.597 12278 Z= 0.260 Chirality : 0.039 0.322 1498 Planarity : 0.003 0.026 1522 Dihedral : 6.396 85.997 1284 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.72 % Allowed : 17.27 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.27), residues: 1122 helix: 3.04 (0.20), residues: 710 sheet: -0.09 (0.63), residues: 70 loop : -1.74 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 408 HIS 0.002 0.000 HIS A 248 PHE 0.012 0.001 PHE A 710 TYR 0.007 0.001 TYR B 228 ARG 0.006 0.000 ARG A 606 *********************** 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 96 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 529 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7711 (mpp) REVERT: B 250 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7016 (t80) REVERT: B 298 LEU cc_start: 0.9272 (tp) cc_final: 0.8942 (tt) REVERT: B 471 LYS cc_start: 0.8010 (mttt) cc_final: 0.7753 (mtpt) outliers start: 17 outliers final: 11 residues processed: 89 average time/residue: 0.2023 time to fit residues: 26.3703 Evaluate side-chains 88 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 705 LEU Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 469 GLU 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 38 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 110 optimal weight: 0.0970 chunk 43 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.101894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078338 restraints weight = 19994.790| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.84 r_work: 0.3132 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9050 Z= 0.166 Angle : 0.545 12.100 12278 Z= 0.269 Chirality : 0.038 0.158 1498 Planarity : 0.003 0.024 1522 Dihedral : 6.349 84.842 1284 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.26), residues: 1122 helix: 3.09 (0.20), residues: 698 sheet: -0.10 (0.64), residues: 70 loop : -1.70 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 408 HIS 0.004 0.001 HIS A 676 PHE 0.013 0.001 PHE A 710 TYR 0.009 0.001 TYR B 433 ARG 0.004 0.000 ARG B 683 *********************** 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: 17 poor density : 75 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 529 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7700 (mpp) REVERT: B 298 LEU cc_start: 0.9268 (tp) cc_final: 0.8951 (tt) REVERT: B 471 LYS cc_start: 0.8086 (mttt) cc_final: 0.7744 (mtpt) outliers start: 17 outliers final: 15 residues processed: 88 average time/residue: 0.1910 time to fit residues: 24.9284 Evaluate side-chains 89 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 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 469 GLU 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 59 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 52 optimal weight: 0.0010 chunk 109 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.101973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078603 restraints weight = 19967.530| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.82 r_work: 0.3134 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2923 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= 0.167 Angle : 0.548 12.524 12278 Z= 0.271 Chirality : 0.038 0.156 1498 Planarity : 0.003 0.025 1522 Dihedral : 6.319 85.049 1284 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.82 % Allowed : 17.78 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.26), residues: 1122 helix: 3.08 (0.20), residues: 698 sheet: -0.12 (0.63), residues: 70 loop : -1.70 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 408 HIS 0.003 0.001 HIS A 248 PHE 0.012 0.001 PHE A 710 TYR 0.008 0.001 TYR B 228 ARG 0.004 0.000 ARG B 683 ********************** 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 90 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 529 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7638 (mpp) REVERT: B 298 LEU cc_start: 0.9275 (tp) cc_final: 0.8957 (tt) REVERT: B 471 LYS cc_start: 0.8090 (mttt) cc_final: 0.7732 (mtpt) outliers start: 18 outliers final: 15 residues processed: 85 average time/residue: 0.1743 time to fit residues: 22.3060 Evaluate side-chains 88 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 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 469 GLU 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 99 optimal weight: 5.9990 chunk 91 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.101422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.077942 restraints weight = 19962.164| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.82 r_work: 0.3125 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9050 Z= 0.169 Angle : 0.549 12.556 12278 Z= 0.272 Chirality : 0.038 0.155 1498 Planarity : 0.003 0.026 1522 Dihedral : 6.266 84.387 1284 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.72 % Allowed : 17.78 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.26), residues: 1122 helix: 3.07 (0.20), residues: 698 sheet: -0.13 (0.64), residues: 70 loop : -1.72 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 408 HIS 0.003 0.001 HIS A 248 PHE 0.013 0.001 PHE A 710 TYR 0.008 0.001 TYR B 228 ARG 0.004 0.000 ARG A 606 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3789.32 seconds wall clock time: 67 minutes 24.91 seconds (4044.91 seconds total)