Starting phenix.real_space_refine on Sat Aug 23 06:05:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ors_17131/08_2025/8ors_17131.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ors_17131/08_2025/8ors_17131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ors_17131/08_2025/8ors_17131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ors_17131/08_2025/8ors_17131.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ors_17131/08_2025/8ors_17131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ors_17131/08_2025/8ors_17131.map" } resolution = 4.3 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= 0.001 sd= 0.003 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 4 5.49 5 S 32 5.16 5 C 6434 2.51 5 N 1742 2.21 5 O 1912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10124 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "B" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.04, per 1000 atoms: 0.20 Number of scatterers: 10124 At special positions: 0 Unit cell: (91.2156, 97.731, 111.848, 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 32 16.00 P 4 15.00 O 1912 8.00 N 1742 7.00 C 6434 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: 0.90 Conformation dependent library (CDL) restraints added in 402.8 milliseconds Enol-peptide restraints added in 0.0 nanoseconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 17 sheets defined 39.3% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 67 through 79 Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.996A pdb=" N TYR A 136 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 176 through 192 removed outlier: 5.949A pdb=" N ASN A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 221 removed outlier: 3.846A pdb=" N SER A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 299 through 305 removed outlier: 4.439A pdb=" N GLY A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 438 through 443 removed outlier: 4.337A pdb=" N ASN A 442 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 520 through 523 removed outlier: 3.596A pdb=" N GLN A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 523' Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 532 through 559 removed outlier: 3.573A pdb=" N ILE A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A 554 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 586 Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.606A pdb=" N TRP A 590 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS A 591 " --> pdb=" O ASN A 588 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 592 " --> pdb=" O TRP A 589 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 594 " --> pdb=" O HIS A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 616 removed outlier: 3.541A pdb=" N SER A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 removed outlier: 3.796A pdb=" N ARG A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 667 through 684 removed outlier: 4.073A pdb=" N ALA A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 672 " --> pdb=" O TRP A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'B' and resid 67 through 79 Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.504A pdb=" N ASP B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 176 through 192 removed outlier: 5.873A pdb=" N ASN B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TYR B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 221 removed outlier: 3.935A pdb=" N SER B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 352 through 361 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 438 through 443 removed outlier: 4.107A pdb=" N ASN B 442 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 468 Processing helix chain 'B' and resid 520 through 532 Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 532 through 559 removed outlier: 3.953A pdb=" N GLN B 554 " --> pdb=" O ILE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 586 removed outlier: 3.670A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 593 removed outlier: 4.351A pdb=" N TRP B 590 " --> pdb=" O ALA B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 599 removed outlier: 3.611A pdb=" N VAL B 598 " --> pdb=" O VAL B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 616 Processing helix chain 'B' and resid 616 through 622 removed outlier: 4.247A pdb=" N ARG B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 Processing helix chain 'B' and resid 668 through 684 Processing helix chain 'B' and resid 686 through 691 Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 308 removed outlier: 6.272A pdb=" N ILE A 83 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL A 308 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 85 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N THR A 56 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N LYS A 342 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASP A 58 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL A 344 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL A 60 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A 346 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 62 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 328 " --> pdb=" O HIS A 336 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLY A 325 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE A 316 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN A 327 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308 removed outlier: 6.272A pdb=" N ILE A 83 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL A 308 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 85 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N THR A 56 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N LYS A 342 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASP A 58 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL A 344 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL A 60 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A 346 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 62 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 128 removed outlier: 3.577A pdb=" N HIS A 144 " --> pdb=" O TRP A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.546A pdb=" N VAL A 260 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA A 426 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN A 450 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 428 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 481 " --> pdb=" O PRO A 393 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.546A pdb=" N VAL A 260 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA A 426 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN A 450 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 428 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 481 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 392 " --> pdb=" O HIS A 624 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA7, first strand: chain 'A' and resid 362 through 363 Processing sheet with id=AA8, first strand: chain 'A' and resid 385 through 387 removed outlier: 5.713A pdb=" N GLY A 490 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 305 through 308 removed outlier: 6.427A pdb=" N ILE B 83 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL B 308 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 85 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE B 59 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU B 86 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE B 61 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 60 " --> pdb=" O GLU B 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 124 through 128 removed outlier: 3.506A pdb=" N HIS B 144 " --> pdb=" O TRP B 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 158 through 159 removed outlier: 4.424A pdb=" N TYR B 266 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AB4, first strand: chain 'B' and resid 312 through 318 removed outlier: 3.528A pdb=" N ASP B 314 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ASN B 327 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE B 316 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY B 325 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE B 318 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA B 323 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 338 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 328 " --> pdb=" O HIS B 336 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 336 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 362 through 363 Processing sheet with id=AB6, first strand: chain 'B' and resid 385 through 387 removed outlier: 5.508A pdb=" N THR B 385 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE B 492 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 449 through 455 removed outlier: 3.608A pdb=" N THR B 478 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 481 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 564 " --> pdb=" O HIS B 400 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 449 through 455 removed outlier: 3.608A pdb=" N THR B 478 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 481 " --> pdb=" O PRO B 393 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1056 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: 1.56 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3334 1.34 - 1.46: 2113 1.46 - 1.57: 4868 1.57 - 1.69: 5 1.69 - 1.81: 60 Bond restraints: 10380 Sorted by residual: bond pdb=" O3P FAD A 901 " pdb=" P FAD A 901 " ideal model delta sigma weight residual 1.660 1.584 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" O3P FAD B 901 " pdb=" P FAD B 901 " ideal model delta sigma weight residual 1.660 1.584 0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" O5' FAD B 901 " pdb=" P FAD B 901 " ideal model delta sigma weight residual 1.637 1.573 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O5' FAD A 901 " pdb=" P FAD A 901 " ideal model delta sigma weight residual 1.637 1.574 0.063 2.00e-02 2.50e+03 9.88e+00 bond pdb=" O5B FAD B 901 " pdb=" PA FAD B 901 " ideal model delta sigma weight residual 1.634 1.572 0.062 2.00e-02 2.50e+03 9.70e+00 ... (remaining 10375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 13869 1.56 - 3.13: 253 3.13 - 4.69: 38 4.69 - 6.25: 11 6.25 - 7.82: 7 Bond angle restraints: 14178 Sorted by residual: angle pdb=" N VAL B 324 " pdb=" CA VAL B 324 " pdb=" C VAL B 324 " ideal model delta sigma weight residual 113.43 109.58 3.85 1.09e+00 8.42e-01 1.25e+01 angle pdb=" CA GLY B 325 " pdb=" C GLY B 325 " pdb=" O GLY B 325 " ideal model delta sigma weight residual 121.62 118.25 3.37 9.80e-01 1.04e+00 1.18e+01 angle pdb=" N GLY A 401 " pdb=" CA GLY A 401 " pdb=" C GLY A 401 " ideal model delta sigma weight residual 110.56 115.00 -4.44 1.36e+00 5.41e-01 1.07e+01 angle pdb=" O1P FAD A 901 " pdb=" P FAD A 901 " pdb=" O2P FAD A 901 " ideal model delta sigma weight residual 122.50 114.68 7.82 3.00e+00 1.11e-01 6.79e+00 angle pdb=" O1P FAD B 901 " pdb=" P FAD B 901 " pdb=" O2P FAD B 901 " ideal model delta sigma weight residual 122.50 115.14 7.36 3.00e+00 1.11e-01 6.03e+00 ... (remaining 14173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.27: 5844 24.27 - 48.55: 265 48.55 - 72.82: 28 72.82 - 97.10: 8 97.10 - 121.37: 1 Dihedral angle restraints: 6146 sinusoidal: 2426 harmonic: 3720 Sorted by residual: dihedral pdb=" O5' FAD B 901 " pdb=" O3P FAD B 901 " pdb=" P FAD B 901 " pdb=" PA FAD B 901 " ideal model delta sinusoidal sigma weight residual 298.23 176.86 121.37 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" CA ASN B 666 " pdb=" C ASN B 666 " pdb=" N THR B 667 " pdb=" CA THR B 667 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASN A 666 " pdb=" C ASN A 666 " pdb=" N THR A 667 " pdb=" CA THR A 667 " ideal model delta harmonic sigma weight residual -180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 6143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 975 0.033 - 0.065: 370 0.065 - 0.098: 137 0.098 - 0.131: 84 0.131 - 0.163: 6 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA ILE B 459 " pdb=" N ILE B 459 " pdb=" C ILE B 459 " pdb=" CB ILE B 459 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" C2B FAD A 901 " pdb=" C1B FAD A 901 " pdb=" C3B FAD A 901 " pdb=" O2B FAD A 901 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE A 459 " pdb=" N ILE A 459 " pdb=" C ILE A 459 " pdb=" CB ILE A 459 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 1569 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 569 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 570 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 569 " 0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 570 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 570 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 570 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 602 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO B 603 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 603 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 603 " 0.018 5.00e-02 4.00e+02 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 194 2.68 - 3.23: 9739 3.23 - 3.79: 15397 3.79 - 4.34: 21018 4.34 - 4.90: 35262 Nonbonded interactions: 81610 Sorted by model distance: nonbonded pdb=" OD1 ASN B 416 " pdb=" OG1 THR B 418 " model vdw 2.121 3.040 nonbonded pdb=" O GLY B 149 " pdb=" OG1 THR B 152 " model vdw 2.160 3.040 nonbonded pdb=" O GLY A 349 " pdb=" OG1 THR A 353 " model vdw 2.188 3.040 nonbonded pdb=" O GLY A 149 " pdb=" OG1 THR A 152 " model vdw 2.209 3.040 nonbonded pdb=" NZ LYS B 644 " pdb=" O GLN B 649 " model vdw 2.253 3.120 ... (remaining 81605 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.003 0.076 10380 Z= 0.165 Angle : 0.551 7.815 14178 Z= 0.280 Chirality : 0.045 0.163 1572 Planarity : 0.004 0.044 1844 Dihedral : 13.613 121.372 3786 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 0.02 (0.24), residues: 1294 helix: 1.08 (0.27), residues: 394 sheet: -0.35 (0.40), residues: 190 loop : -0.44 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 447 TYR 0.007 0.001 TYR B 74 PHE 0.014 0.001 PHE A 365 TRP 0.008 0.001 TRP A 125 HIS 0.002 0.000 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00327 (10380) covalent geometry : angle 0.55110 (14178) hydrogen bonds : bond 0.22776 ( 367) hydrogen bonds : angle 8.04280 ( 1056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.382 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0933 time to fit residues: 6.9343 Evaluate side-chains 37 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN A 400 HIS B 138 ASN B 547 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.051908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.037954 restraints weight = 31299.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.039282 restraints weight = 18991.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.040174 restraints weight = 13778.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.040721 restraints weight = 11291.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.040951 restraints weight = 9994.877| |-----------------------------------------------------------------------------| r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10380 Z= 0.184 Angle : 0.611 10.897 14178 Z= 0.312 Chirality : 0.048 0.169 1572 Planarity : 0.005 0.044 1844 Dihedral : 7.829 107.167 1514 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.24), residues: 1294 helix: 0.98 (0.27), residues: 400 sheet: -0.43 (0.37), residues: 220 loop : -0.70 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 279 TYR 0.014 0.001 TYR A 491 PHE 0.015 0.002 PHE B 486 TRP 0.011 0.002 TRP A 125 HIS 0.004 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00431 (10380) covalent geometry : angle 0.61147 (14178) hydrogen bonds : bond 0.05090 ( 367) hydrogen bonds : angle 5.56903 ( 1056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.266 Fit side-chains REVERT: B 179 ASP cc_start: 0.6458 (t0) cc_final: 0.6098 (t0) REVERT: B 402 GLU cc_start: 0.8361 (mp0) cc_final: 0.8086 (mp0) REVERT: B 566 GLU cc_start: 0.5952 (tp30) cc_final: 0.5699 (pt0) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0657 time to fit residues: 5.0798 Evaluate side-chains 39 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.050798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.037501 restraints weight = 31281.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.038753 restraints weight = 18930.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.039586 restraints weight = 13804.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.040093 restraints weight = 11330.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.040463 restraints weight = 10070.109| |-----------------------------------------------------------------------------| r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10380 Z= 0.216 Angle : 0.652 12.388 14178 Z= 0.331 Chirality : 0.049 0.176 1572 Planarity : 0.005 0.045 1844 Dihedral : 7.401 103.146 1514 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.24), residues: 1294 helix: 0.76 (0.26), residues: 400 sheet: -0.75 (0.36), residues: 220 loop : -0.81 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 156 TYR 0.015 0.002 TYR A 367 PHE 0.024 0.002 PHE A 486 TRP 0.013 0.002 TRP A 125 HIS 0.003 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00508 (10380) covalent geometry : angle 0.65223 (14178) hydrogen bonds : bond 0.05113 ( 367) hydrogen bonds : angle 5.44024 ( 1056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.287 Fit side-chains REVERT: B 402 GLU cc_start: 0.8428 (mp0) cc_final: 0.8103 (mp0) outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.0890 time to fit residues: 6.3485 Evaluate side-chains 34 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 87 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 80 optimal weight: 40.0000 chunk 61 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.051512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.037912 restraints weight = 31161.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.039260 restraints weight = 18726.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.040154 restraints weight = 13575.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.040689 restraints weight = 11044.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.041073 restraints weight = 9809.606| |-----------------------------------------------------------------------------| r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10380 Z= 0.158 Angle : 0.600 11.100 14178 Z= 0.303 Chirality : 0.048 0.167 1572 Planarity : 0.005 0.046 1844 Dihedral : 6.901 100.101 1514 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.24), residues: 1294 helix: 0.91 (0.26), residues: 400 sheet: -0.84 (0.36), residues: 222 loop : -0.79 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.012 0.001 TYR A 491 PHE 0.020 0.002 PHE B 365 TRP 0.008 0.001 TRP A 125 HIS 0.002 0.001 HIS A 591 Details of bonding type rmsd covalent geometry : bond 0.00372 (10380) covalent geometry : angle 0.59985 (14178) hydrogen bonds : bond 0.04427 ( 367) hydrogen bonds : angle 5.18251 ( 1056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.250 Fit side-chains REVERT: A 75 LEU cc_start: 0.8761 (mt) cc_final: 0.8547 (mp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0827 time to fit residues: 5.9416 Evaluate side-chains 36 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 126 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 11 optimal weight: 0.0770 chunk 54 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 overall best weight: 3.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 562 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.051976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.038035 restraints weight = 31425.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.039426 restraints weight = 18720.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.040319 restraints weight = 13439.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.040894 restraints weight = 10945.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.041226 restraints weight = 9641.349| |-----------------------------------------------------------------------------| r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10380 Z= 0.141 Angle : 0.582 10.709 14178 Z= 0.292 Chirality : 0.047 0.162 1572 Planarity : 0.005 0.043 1844 Dihedral : 6.684 99.750 1514 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.24), residues: 1294 helix: 1.00 (0.26), residues: 400 sheet: -0.74 (0.37), residues: 220 loop : -0.81 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.011 0.001 TYR A 491 PHE 0.016 0.001 PHE A 486 TRP 0.008 0.001 TRP A 125 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00331 (10380) covalent geometry : angle 0.58190 (14178) hydrogen bonds : bond 0.04157 ( 367) hydrogen bonds : angle 5.01631 ( 1056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.385 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0758 time to fit residues: 5.6132 Evaluate side-chains 36 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.051171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.037656 restraints weight = 31427.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.038938 restraints weight = 19064.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.039825 restraints weight = 13966.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.040372 restraints weight = 11407.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.040766 restraints weight = 10075.852| |-----------------------------------------------------------------------------| r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10380 Z= 0.177 Angle : 0.609 12.034 14178 Z= 0.307 Chirality : 0.048 0.169 1572 Planarity : 0.005 0.044 1844 Dihedral : 6.772 99.448 1514 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.24), residues: 1294 helix: 0.88 (0.26), residues: 400 sheet: -0.86 (0.36), residues: 220 loop : -0.86 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.013 0.001 TYR A 491 PHE 0.021 0.002 PHE A 593 TRP 0.008 0.001 TRP A 125 HIS 0.004 0.001 HIS A 591 Details of bonding type rmsd covalent geometry : bond 0.00419 (10380) covalent geometry : angle 0.60850 (14178) hydrogen bonds : bond 0.04415 ( 367) hydrogen bonds : angle 5.05892 ( 1056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.296 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1003 time to fit residues: 6.6942 Evaluate side-chains 35 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.052320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.038341 restraints weight = 31261.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.039746 restraints weight = 18530.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.040672 restraints weight = 13269.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.041219 restraints weight = 10749.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.041603 restraints weight = 9523.251| |-----------------------------------------------------------------------------| r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10380 Z= 0.129 Angle : 0.581 10.700 14178 Z= 0.290 Chirality : 0.047 0.159 1572 Planarity : 0.005 0.043 1844 Dihedral : 6.641 99.723 1514 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.24), residues: 1294 helix: 0.95 (0.26), residues: 400 sheet: -0.83 (0.36), residues: 222 loop : -0.79 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.011 0.001 TYR A 491 PHE 0.015 0.001 PHE A 477 TRP 0.007 0.001 TRP B 125 HIS 0.002 0.001 HIS A 591 Details of bonding type rmsd covalent geometry : bond 0.00299 (10380) covalent geometry : angle 0.58055 (14178) hydrogen bonds : bond 0.04013 ( 367) hydrogen bonds : angle 4.93570 ( 1056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.396 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0671 time to fit residues: 5.1304 Evaluate side-chains 39 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 61 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.051616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.037843 restraints weight = 31223.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.039199 restraints weight = 18807.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.040062 restraints weight = 13541.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.040603 restraints weight = 11078.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.040931 restraints weight = 9793.475| |-----------------------------------------------------------------------------| r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10380 Z= 0.166 Angle : 0.607 11.832 14178 Z= 0.304 Chirality : 0.048 0.182 1572 Planarity : 0.005 0.044 1844 Dihedral : 6.726 99.942 1514 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.24), residues: 1294 helix: 0.86 (0.26), residues: 400 sheet: -0.93 (0.36), residues: 222 loop : -0.86 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.013 0.001 TYR A 491 PHE 0.015 0.002 PHE A 477 TRP 0.008 0.001 TRP B 125 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00392 (10380) covalent geometry : angle 0.60706 (14178) hydrogen bonds : bond 0.04319 ( 367) hydrogen bonds : angle 4.98465 ( 1056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.266 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0814 time to fit residues: 5.9088 Evaluate side-chains 36 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 83 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 5 optimal weight: 0.0770 chunk 50 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 0.0040 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 overall best weight: 3.8156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.052090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.038299 restraints weight = 31161.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.039605 restraints weight = 19024.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.040463 restraints weight = 13906.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.041020 restraints weight = 11384.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.041163 restraints weight = 10060.652| |-----------------------------------------------------------------------------| r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10380 Z= 0.137 Angle : 0.582 11.037 14178 Z= 0.292 Chirality : 0.047 0.164 1572 Planarity : 0.005 0.044 1844 Dihedral : 6.622 101.020 1514 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.24), residues: 1294 helix: 0.95 (0.26), residues: 400 sheet: -0.85 (0.36), residues: 222 loop : -0.83 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.012 0.001 TYR A 367 PHE 0.014 0.001 PHE A 477 TRP 0.008 0.001 TRP B 125 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00322 (10380) covalent geometry : angle 0.58196 (14178) hydrogen bonds : bond 0.04082 ( 367) hydrogen bonds : angle 4.92208 ( 1056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.252 Fit side-chains REVERT: B 177 TYR cc_start: 0.7139 (t80) cc_final: 0.6791 (t80) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0739 time to fit residues: 5.5735 Evaluate side-chains 38 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 59 optimal weight: 0.0060 chunk 115 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.052551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.038552 restraints weight = 30773.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.039932 restraints weight = 18396.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.040839 restraints weight = 13252.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.041422 restraints weight = 10776.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.041769 restraints weight = 9480.805| |-----------------------------------------------------------------------------| r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10380 Z= 0.120 Angle : 0.561 10.100 14178 Z= 0.282 Chirality : 0.046 0.155 1572 Planarity : 0.005 0.043 1844 Dihedral : 6.513 102.206 1514 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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 aren not related in a simple way. whole: -0.35 (0.24), residues: 1294 helix: 1.03 (0.26), residues: 400 sheet: -0.74 (0.37), residues: 222 loop : -0.79 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.012 0.001 TYR A 367 PHE 0.014 0.001 PHE A 477 TRP 0.008 0.001 TRP B 125 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00280 (10380) covalent geometry : angle 0.56079 (14178) hydrogen bonds : bond 0.03863 ( 367) hydrogen bonds : angle 4.84420 ( 1056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.280 Fit side-chains REVERT: B 146 MET cc_start: 0.6523 (mtp) cc_final: 0.6251 (mtp) REVERT: B 177 TYR cc_start: 0.7059 (t80) cc_final: 0.6744 (t80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0713 time to fit residues: 5.4965 Evaluate side-chains 39 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 18 optimal weight: 0.0030 overall best weight: 3.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.052388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.038414 restraints weight = 31183.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.039785 restraints weight = 18592.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.040685 restraints weight = 13351.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.041291 restraints weight = 10844.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.041631 restraints weight = 9496.890| |-----------------------------------------------------------------------------| r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10380 Z= 0.137 Angle : 0.575 10.628 14178 Z= 0.288 Chirality : 0.047 0.159 1572 Planarity : 0.005 0.044 1844 Dihedral : 6.512 102.984 1514 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.24), residues: 1294 helix: 1.00 (0.26), residues: 400 sheet: -0.76 (0.36), residues: 222 loop : -0.81 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.012 0.001 TYR A 367 PHE 0.023 0.001 PHE B 365 TRP 0.008 0.001 TRP B 125 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00325 (10380) covalent geometry : angle 0.57477 (14178) hydrogen bonds : bond 0.03990 ( 367) hydrogen bonds : angle 4.85746 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1300.70 seconds wall clock time: 23 minutes 25.63 seconds (1405.63 seconds total)