Starting phenix.real_space_refine on Thu Jul 2 14:55:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hf4_34712/07_2026/8hf4_34712.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hf4_34712/07_2026/8hf4_34712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hf4_34712/07_2026/8hf4_34712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hf4_34712/07_2026/8hf4_34712.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hf4_34712/07_2026/8hf4_34712.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hf4_34712/07_2026/8hf4_34712.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hf4_34712/07_2026/8hf4_34712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hf4_34712/07_2026/8hf4_34712.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 30 5.16 5 C 5732 2.51 5 N 1462 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 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.73, per 1000 atoms: 0.19 Number of scatterers: 8916 At special positions: 0 Unit cell: (82.368, 81.51, 140.712, 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 30 16.00 P 6 15.00 O 1686 8.00 N 1462 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: 0.69 Conformation dependent library (CDL) restraints added in 462.6 milliseconds 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: 49 helices and 4 sheets defined 70.4% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 157 through 164 removed outlier: 3.511A pdb=" N VAL A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 195 removed outlier: 3.574A pdb=" N ILE A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 250 removed outlier: 3.720A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 4.038A pdb=" N PHE A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 258 " --> pdb=" O MET A 254 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 260' Processing helix chain 'A' and resid 261 through 276 removed outlier: 3.663A pdb=" N ILE A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 280 through 288 removed outlier: 3.742A pdb=" N LEU A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.640A pdb=" N MET A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 325 removed outlier: 3.979A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 353 removed outlier: 3.671A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 362 through 416 removed outlier: 4.021A pdb=" N ARG A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 459 removed outlier: 3.544A pdb=" N TYR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.733A pdb=" N ILE A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.603A pdb=" N LEU A 463 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.658A pdb=" N VAL A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 removed outlier: 3.501A pdb=" N LEU A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) 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: 3.834A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 removed outlier: 3.927A pdb=" N ALA A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 removed outlier: 4.390A pdb=" N ALA A 681 " --> pdb=" O ARG A 677 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 683' Processing helix chain 'A' and resid 700 through 706 Processing helix chain 'A' and resid 709 through 717 Processing helix chain 'B' and resid 157 through 163 removed outlier: 3.979A pdb=" N LYS B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 195 removed outlier: 3.533A pdb=" N ASN B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 185 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 192 " --> pdb=" O TYR B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 203 through 251 removed outlier: 3.702A pdb=" N ILE B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 211 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 removed outlier: 4.041A pdb=" N PHE B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 258 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.732A 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: 3.633A pdb=" N ILE B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 304 removed outlier: 3.815A pdb=" N ILE B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 Processing helix chain 'B' and resid 313 through 325 removed outlier: 4.019A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE B 325 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 353 removed outlier: 3.894A pdb=" N PHE B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU B 330 " --> pdb=" O MET B 326 " (cutoff:3.500A) removed outlier: 3.697A 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: 4.002A pdb=" N ARG B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 459 removed outlier: 3.978A pdb=" N VAL B 432 " --> pdb=" O ASN B 428 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR B 433 " --> pdb=" O THR B 429 " (cutoff:3.500A) Proline residue: B 437 - end of helix removed outlier: 4.056A pdb=" N THR B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 522 through 531 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 Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 623 through 638 removed outlier: 3.702A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 666 removed outlier: 3.829A pdb=" N ALA B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.787A pdb=" N GLU B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG B 683 " --> pdb=" O THR B 679 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 684 " --> pdb=" O ILE B 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 678 through 684' Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.589A pdb=" N LEU B 704 " --> pdb=" O LYS B 700 " (cutoff:3.500A) removed outlier: 3.756A 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: 4.062A pdb=" N LEU A 500 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL A 489 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 542 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 487 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 540 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 489 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLN A 538 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 562 removed outlier: 6.577A pdb=" N ASN A 561 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASP A 646 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 513 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 512 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N VAL A 688 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA A 514 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU A 690 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 516 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 699 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU A 697 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 504 through 505 removed outlier: 3.792A pdb=" N LEU B 505 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N PHE B 486 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N SER B 542 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLN B 488 " --> pdb=" O GLU B 540 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU B 540 " --> pdb=" O GLN B 488 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 538 " --> pdb=" O HIS B 490 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 560 through 563 removed outlier: 6.795A pdb=" N ASN B 561 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE B 643 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE B 674 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 645 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 513 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL B 688 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA B 514 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU B 690 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 516 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU B 697 " --> pdb=" O VAL B 689 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1575 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: 1.06 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 2896 1.37 - 1.54: 6074 1.54 - 1.72: 22 1.72 - 1.89: 56 1.89 - 2.07: 2 Bond restraints: 9050 Sorted by residual: bond pdb=" C4 AGS A 801 " pdb=" C5 AGS A 801 " ideal model delta sigma weight residual 1.386 1.458 -0.072 1.00e-02 1.00e+04 5.25e+01 bond pdb=" C4 AGS B 801 " pdb=" C5 AGS B 801 " ideal model delta sigma weight residual 1.386 1.458 -0.072 1.00e-02 1.00e+04 5.21e+01 bond pdb=" PG AGS A 801 " pdb=" S1G AGS A 801 " ideal model delta sigma weight residual 1.949 2.070 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" PG AGS B 801 " pdb=" S1G AGS B 801 " ideal model delta sigma weight residual 1.949 2.069 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C5 AGS B 801 " pdb=" C6 AGS B 801 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.61e+01 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 11918 1.89 - 3.78: 260 3.78 - 5.67: 72 5.67 - 7.56: 12 7.56 - 9.45: 16 Bond angle restraints: 12278 Sorted by residual: angle pdb=" C5 AGS A 801 " pdb=" C4 AGS A 801 " pdb=" N3 AGS A 801 " ideal model delta sigma weight residual 126.80 118.84 7.96 7.41e-01 1.82e+00 1.16e+02 angle pdb=" C5 AGS B 801 " pdb=" C4 AGS B 801 " pdb=" N3 AGS B 801 " ideal model delta sigma weight residual 126.80 118.87 7.93 7.41e-01 1.82e+00 1.15e+02 angle pdb=" C4 AGS B 801 " pdb=" C5 AGS B 801 " pdb=" N7 AGS B 801 " ideal model delta sigma weight residual 110.73 106.97 3.76 4.52e-01 4.89e+00 6.92e+01 angle pdb=" C5 AGS B 801 " pdb=" N7 AGS B 801 " pdb=" C8 AGS B 801 " ideal model delta sigma weight residual 103.67 107.21 -3.54 4.26e-01 5.51e+00 6.92e+01 angle pdb=" C4 AGS A 801 " pdb=" C5 AGS A 801 " pdb=" N7 AGS A 801 " ideal model delta sigma weight residual 110.73 106.97 3.76 4.52e-01 4.89e+00 6.91e+01 ... (remaining 12273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 5100 23.82 - 47.64: 335 47.64 - 71.46: 20 71.46 - 95.27: 11 95.27 - 119.09: 2 Dihedral angle restraints: 5468 sinusoidal: 2174 harmonic: 3294 Sorted by residual: dihedral pdb=" C PHE B 673 " pdb=" N PHE B 673 " pdb=" CA PHE B 673 " pdb=" CB PHE B 673 " ideal model delta harmonic sigma weight residual -122.60 -111.61 -10.99 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" O1A AGS A 801 " pdb=" O3A AGS A 801 " pdb=" PA AGS A 801 " pdb=" PB AGS A 801 " ideal model delta sinusoidal sigma weight residual -67.73 51.36 -119.09 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" O1A AGS B 801 " pdb=" O3A AGS B 801 " pdb=" PA AGS B 801 " pdb=" PB AGS B 801 " ideal model delta sinusoidal sigma weight residual -67.73 51.35 -119.08 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 5465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1387 0.076 - 0.151: 89 0.151 - 0.227: 19 0.227 - 0.302: 3 0.302 - 0.378: 4 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA SER B 519 " pdb=" N SER B 519 " pdb=" C SER B 519 " pdb=" CB SER B 519 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA LYS B 528 " pdb=" N LYS B 528 " pdb=" C LYS B 528 " pdb=" CB LYS B 528 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB ILE A 600 " pdb=" CA ILE A 600 " pdb=" CG1 ILE A 600 " pdb=" CG2 ILE A 600 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 1499 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 187 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C TYR B 187 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR B 187 " 0.021 2.00e-02 2.50e+03 pdb=" N TYR B 188 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 563 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO B 564 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 564 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 564 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 436 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO B 437 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 437 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 437 " -0.030 5.00e-02 4.00e+02 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1015 2.75 - 3.28: 9189 3.28 - 3.82: 14353 3.82 - 4.36: 15601 4.36 - 4.90: 27944 Nonbonded interactions: 68102 Sorted by model distance: nonbonded pdb=" OD1 ASP B 653 " pdb=" OG1 THR B 656 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR A 524 " pdb=" O2G AGS A 801 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR B 175 " pdb=" OE1 GLN B 226 " model vdw 2.263 3.040 nonbonded pdb=" O SER B 519 " pdb=" O1B AGS B 801 " model vdw 2.277 3.040 nonbonded pdb=" O ILE B 207 " pdb=" N SER B 209 " model vdw 2.293 3.120 ... (remaining 68097 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: 1.120 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.390 Find NCS groups from input model: 0.140 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 : 0.006 0.121 9050 Z= 0.428 Angle : 0.755 9.449 12278 Z= 0.509 Chirality : 0.048 0.378 1502 Planarity : 0.004 0.054 1522 Dihedral : 14.874 119.092 3344 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.72 % Favored : 94.92 % Rotamer: Outliers : 1.11 % Allowed : 1.41 % Favored : 97.47 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.26), residues: 1122 helix: 2.75 (0.20), residues: 686 sheet: 1.12 (0.69), residues: 72 loop : -1.50 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 677 TYR 0.013 0.001 TYR B 562 PHE 0.030 0.001 PHE B 673 TRP 0.009 0.001 TRP A 408 HIS 0.002 0.001 HIS B 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.43 ( 9050) covalent geometry : angle 0.75483 / 0.51 (12278) hydrogen bonds : bond 0.17133 / 11.55 ( 532) hydrogen bonds : angle 4.96679 / 3.59 ( 1575) *********************** 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 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.363 Fit side-chains REVERT: A 683 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8097 (mtp85) REVERT: B 198 PRO cc_start: 0.8104 (Cg_exo) cc_final: 0.7904 (Cg_endo) REVERT: B 529 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8610 (mtt) outliers start: 11 outliers final: 1 residues processed: 99 average time/residue: 0.4183 time to fit residues: 45.2099 Evaluate side-chains 56 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 683 ARG Chi-restraints excluded: chain B residue 529 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 566 GLN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 GLN B 566 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.086174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.065690 restraints weight = 21993.310| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.28 r_work: 0.3019 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1190 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= 0.157 Angle : 0.569 10.215 12278 Z= 0.297 Chirality : 0.041 0.364 1502 Planarity : 0.003 0.042 1522 Dihedral : 7.332 135.297 1239 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.12 % Allowed : 9.70 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.26), residues: 1122 helix: 2.75 (0.20), residues: 704 sheet: 0.50 (0.64), residues: 80 loop : -1.55 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 677 TYR 0.018 0.001 TYR A 559 PHE 0.012 0.001 PHE A 673 TRP 0.005 0.001 TRP A 408 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 ( 9050) covalent geometry : angle 0.56865 / 0.30 (12278) hydrogen bonds : bond 0.07449 / 4.97 ( 532) hydrogen bonds : angle 3.99137 / 2.91 ( 1575) *********************** 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 82 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.384 Fit side-chains REVERT: A 193 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8074 (mp) REVERT: A 201 MET cc_start: 0.8534 (mtp) cc_final: 0.8298 (mpp) REVERT: A 409 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8213 (tpp) REVERT: A 676 HIS cc_start: 0.8923 (m170) cc_final: 0.8656 (m-70) REVERT: B 201 MET cc_start: 0.6642 (mmm) cc_final: 0.5942 (mmm) REVERT: B 458 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8223 (mp) REVERT: B 599 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7155 (tm-30) outliers start: 21 outliers final: 7 residues processed: 73 average time/residue: 0.4085 time to fit residues: 32.8215 Evaluate side-chains 59 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 676 HIS 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: 0.8980 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 GLN B 488 GLN B 504 ASN B 538 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.086452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.066226 restraints weight = 21684.949| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.23 r_work: 0.3025 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1452 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= 0.133 Angle : 0.527 10.183 12278 Z= 0.270 Chirality : 0.039 0.282 1502 Planarity : 0.003 0.040 1522 Dihedral : 7.243 131.921 1230 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.92 % Allowed : 13.03 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.26), residues: 1122 helix: 2.84 (0.20), residues: 702 sheet: 0.49 (0.63), residues: 80 loop : -1.46 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 677 TYR 0.014 0.001 TYR B 187 PHE 0.008 0.001 PHE A 673 TRP 0.007 0.001 TRP A 408 HIS 0.003 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 9050) covalent geometry : angle 0.52682 / 0.27 (12278) hydrogen bonds : bond 0.06948 / 4.67 ( 532) hydrogen bonds : angle 3.77174 / 2.75 ( 1575) *********************** 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 79 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 193 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7656 (mp) REVERT: A 201 MET cc_start: 0.8427 (mtp) cc_final: 0.8222 (mpp) REVERT: A 604 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8478 (pt) REVERT: A 676 HIS cc_start: 0.8949 (m170) cc_final: 0.8708 (m-70) REVERT: B 201 MET cc_start: 0.7411 (mmm) cc_final: 0.6813 (mmm) REVERT: B 419 MET cc_start: 0.7970 (ptm) cc_final: 0.7648 (ptm) REVERT: B 599 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7197 (tm-30) outliers start: 19 outliers final: 5 residues processed: 70 average time/residue: 0.4264 time to fit residues: 32.9246 Evaluate side-chains 59 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 406 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 52 optimal weight: 0.0050 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.087702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067320 restraints weight = 21811.093| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.27 r_work: 0.3051 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9050 Z= 0.121 Angle : 0.502 8.231 12278 Z= 0.258 Chirality : 0.038 0.198 1502 Planarity : 0.003 0.036 1522 Dihedral : 7.097 124.996 1230 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.63 % Allowed : 14.14 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.26), residues: 1122 helix: 3.01 (0.20), residues: 702 sheet: 0.52 (0.63), residues: 80 loop : -1.50 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 606 TYR 0.012 0.001 TYR A 559 PHE 0.007 0.001 PHE A 673 TRP 0.008 0.001 TRP A 408 HIS 0.002 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 ( 9050) covalent geometry : angle 0.50203 / 0.26 (12278) hydrogen bonds : bond 0.06293 / 4.25 ( 532) hydrogen bonds : angle 3.53559 / 2.58 ( 1575) *********************** 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 89 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 326 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8339 (ptp) REVERT: A 484 MET cc_start: 0.8760 (ttm) cc_final: 0.8515 (ttm) REVERT: A 676 HIS cc_start: 0.8954 (m170) cc_final: 0.8728 (m-70) REVERT: B 201 MET cc_start: 0.7689 (mmm) cc_final: 0.6962 (mmm) REVERT: B 599 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7222 (tm-30) REVERT: B 622 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.6839 (tp) outliers start: 26 outliers final: 10 residues processed: 81 average time/residue: 0.3487 time to fit residues: 31.1633 Evaluate side-chains 66 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 622 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.086552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.066192 restraints weight = 21906.319| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.26 r_work: 0.3027 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1761 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 : 0.504 8.522 12278 Z= 0.259 Chirality : 0.038 0.182 1502 Planarity : 0.003 0.034 1522 Dihedral : 7.022 120.463 1230 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.42 % Allowed : 15.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.26), residues: 1122 helix: 2.98 (0.19), residues: 702 sheet: 0.44 (0.62), residues: 80 loop : -1.48 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 386 TYR 0.011 0.001 TYR B 187 PHE 0.006 0.001 PHE A 673 TRP 0.005 0.001 TRP A 408 HIS 0.003 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 9050) covalent geometry : angle 0.50434 / 0.26 (12278) hydrogen bonds : bond 0.06477 / 4.38 ( 532) hydrogen bonds : angle 3.53030 / 2.59 ( 1575) *********************** 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 79 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.375 Fit side-chains REVERT: A 326 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8395 (ptp) REVERT: A 676 HIS cc_start: 0.8977 (m170) cc_final: 0.8741 (m-70) REVERT: B 201 MET cc_start: 0.7846 (mmm) cc_final: 0.7166 (mtp) REVERT: B 419 MET cc_start: 0.7961 (ptm) cc_final: 0.7386 (ptm) REVERT: B 599 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7167 (tm-30) REVERT: B 676 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.8468 (t70) outliers start: 24 outliers final: 13 residues processed: 70 average time/residue: 0.3516 time to fit residues: 27.1880 Evaluate side-chains 65 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 676 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.084855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.064307 restraints weight = 21977.445| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.26 r_work: 0.2992 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1890 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= 0.145 Angle : 0.516 7.473 12278 Z= 0.266 Chirality : 0.038 0.188 1502 Planarity : 0.003 0.034 1522 Dihedral : 6.999 118.114 1230 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.93 % Allowed : 16.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.26), residues: 1122 helix: 2.97 (0.19), residues: 702 sheet: 0.36 (0.62), residues: 80 loop : -1.51 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 236 TYR 0.012 0.001 TYR B 187 PHE 0.006 0.001 PHE A 673 TRP 0.006 0.001 TRP A 408 HIS 0.005 0.001 HIS B 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 9050) covalent geometry : angle 0.51611 / 0.27 (12278) hydrogen bonds : bond 0.06922 / 4.68 ( 532) hydrogen bonds : angle 3.59444 / 2.62 ( 1575) *********************** 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 81 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 326 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8347 (ptp) REVERT: A 676 HIS cc_start: 0.8982 (m170) cc_final: 0.8769 (m-70) REVERT: B 201 MET cc_start: 0.8043 (mmm) cc_final: 0.7287 (mtp) REVERT: B 676 HIS cc_start: 0.8710 (OUTLIER) cc_final: 0.8492 (t70) outliers start: 29 outliers final: 16 residues processed: 72 average time/residue: 0.3602 time to fit residues: 28.4793 Evaluate side-chains 68 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 676 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: 8.9990 chunk 76 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.084685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.064139 restraints weight = 21984.293| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.26 r_work: 0.2993 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1980 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= 0.137 Angle : 0.518 8.452 12278 Z= 0.266 Chirality : 0.038 0.192 1502 Planarity : 0.003 0.036 1522 Dihedral : 6.981 116.221 1230 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.63 % Allowed : 17.37 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.26), residues: 1122 helix: 2.96 (0.20), residues: 702 sheet: 0.30 (0.62), residues: 80 loop : -1.49 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 677 TYR 0.011 0.001 TYR B 187 PHE 0.006 0.001 PHE A 673 TRP 0.006 0.001 TRP A 408 HIS 0.003 0.001 HIS B 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 9050) covalent geometry : angle 0.51777 / 0.27 (12278) hydrogen bonds : bond 0.06888 / 4.67 ( 532) hydrogen bonds : angle 3.59365 / 2.62 ( 1575) *********************** 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 77 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 676 HIS cc_start: 0.9011 (m170) cc_final: 0.8798 (m-70) REVERT: B 201 MET cc_start: 0.8141 (mmm) cc_final: 0.7415 (mtp) outliers start: 26 outliers final: 23 residues processed: 70 average time/residue: 0.3617 time to fit residues: 28.1156 Evaluate side-chains 73 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 676 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.086523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.066145 restraints weight = 21611.297| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.25 r_work: 0.3027 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2039 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= 0.120 Angle : 0.503 8.825 12278 Z= 0.256 Chirality : 0.037 0.200 1502 Planarity : 0.003 0.036 1522 Dihedral : 6.868 110.558 1230 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.63 % Allowed : 18.18 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.26), residues: 1122 helix: 3.05 (0.20), residues: 702 sheet: 0.37 (0.63), residues: 80 loop : -1.49 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 606 TYR 0.010 0.001 TYR B 187 PHE 0.007 0.001 PHE A 673 TRP 0.006 0.001 TRP A 408 HIS 0.003 0.001 HIS B 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 ( 9050) covalent geometry : angle 0.50269 / 0.26 (12278) hydrogen bonds : bond 0.06294 / 4.27 ( 532) hydrogen bonds : angle 3.47046 / 2.53 ( 1575) *********************** 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 84 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 676 HIS cc_start: 0.8979 (m170) cc_final: 0.8768 (m-70) REVERT: B 201 MET cc_start: 0.8317 (mmm) cc_final: 0.7631 (mtp) outliers start: 26 outliers final: 20 residues processed: 78 average time/residue: 0.3437 time to fit residues: 29.7629 Evaluate side-chains 72 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 676 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 15 optimal weight: 0.0970 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.082276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.061761 restraints weight = 22003.939| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.18 r_work: 0.2935 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9050 Z= 0.187 Angle : 0.588 9.571 12278 Z= 0.303 Chirality : 0.040 0.326 1502 Planarity : 0.003 0.036 1522 Dihedral : 6.985 113.206 1230 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.73 % Allowed : 18.08 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.26), residues: 1122 helix: 2.79 (0.19), residues: 704 sheet: 0.20 (0.62), residues: 80 loop : -1.59 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 629 TYR 0.012 0.001 TYR B 187 PHE 0.006 0.001 PHE A 673 TRP 0.010 0.002 TRP A 408 HIS 0.004 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 9050) covalent geometry : angle 0.58804 / 0.30 (12278) hydrogen bonds : bond 0.07722 / 5.23 ( 532) hydrogen bonds : angle 3.77768 / 2.76 ( 1575) *********************** 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 75 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 0.352 Fit side-chains REVERT: B 201 MET cc_start: 0.8418 (mmm) cc_final: 0.7739 (mtp) REVERT: B 368 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7199 (mp10) REVERT: B 676 HIS cc_start: 0.8702 (OUTLIER) cc_final: 0.8468 (t70) outliers start: 27 outliers final: 19 residues processed: 70 average time/residue: 0.3672 time to fit residues: 28.4117 Evaluate side-chains 65 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 676 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.0770 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.083659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063265 restraints weight = 21838.180| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.21 r_work: 0.2966 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2196 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= 0.139 Angle : 0.551 9.834 12278 Z= 0.280 Chirality : 0.039 0.318 1502 Planarity : 0.003 0.035 1522 Dihedral : 6.957 111.556 1230 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.32 % Allowed : 18.79 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.26), residues: 1122 helix: 2.87 (0.19), residues: 702 sheet: 0.23 (0.63), residues: 80 loop : -1.56 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 629 TYR 0.009 0.001 TYR B 187 PHE 0.007 0.001 PHE A 673 TRP 0.002 0.001 TRP A 408 HIS 0.003 0.001 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 9050) covalent geometry : angle 0.55084 / 0.28 (12278) hydrogen bonds : bond 0.07177 / 4.86 ( 532) hydrogen bonds : angle 3.66718 / 2.68 ( 1575) ********************** 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 73 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: B 201 MET cc_start: 0.8529 (mmm) cc_final: 0.7856 (mtp) REVERT: B 599 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7225 (tm-30) REVERT: B 676 HIS cc_start: 0.8729 (OUTLIER) cc_final: 0.8520 (t70) outliers start: 23 outliers final: 19 residues processed: 67 average time/residue: 0.3599 time to fit residues: 26.5721 Evaluate side-chains 69 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 676 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.084980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.064474 restraints weight = 21671.264| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.22 r_work: 0.2993 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9050 Z= 0.130 Angle : 0.540 9.685 12278 Z= 0.275 Chirality : 0.040 0.365 1502 Planarity : 0.003 0.036 1522 Dihedral : 6.859 110.692 1230 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.02 % Allowed : 19.09 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.26), residues: 1122 helix: 2.89 (0.20), residues: 704 sheet: 0.27 (0.63), residues: 80 loop : -1.56 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 629 TYR 0.008 0.001 TYR B 228 PHE 0.006 0.001 PHE A 673 TRP 0.004 0.001 TRP A 408 HIS 0.003 0.001 HIS B 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 9050) covalent geometry : angle 0.53988 / 0.28 (12278) hydrogen bonds : bond 0.06707 / 4.55 ( 532) hydrogen bonds : angle 3.60204 / 2.64 ( 1575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.55 seconds wall clock time: 34 minutes 17.55 seconds (2057.55 seconds total)