Starting phenix.real_space_refine on Fri Feb 14 11:57:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ors_17131/02_2025/8ors_17131.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ors_17131/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ors_17131/02_2025/8ors_17131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ors_17131/02_2025/8ors_17131.map" model { file = "/net/cci-nas-00/data/ceres_data/8ors_17131/02_2025/8ors_17131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ors_17131/02_2025/8ors_17131.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 7.48, per 1000 atoms: 0.74 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.22 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: 3.64 Time building geometry restraints manager: 2.84 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: 0.05 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: 3.360 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 27.290 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.810 ------------------------------------------------------------------------------- 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= 0.220 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 : 7.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.001 TRP A 125 HIS 0.002 0.000 HIS B 92 PHE 0.014 0.001 PHE A 365 TYR 0.007 0.001 TYR B 74 ARG 0.002 0.000 ARG A 447 *********************** 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 : 1.199 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2309 time to fit residues: 17.3776 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 : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 HIS B 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.052704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.038668 restraints weight = 31068.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.039987 restraints weight = 18708.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.040865 restraints weight = 13632.050| |-----------------------------------------------------------------------------| r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.0886 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= 0.219 Angle : 0.576 9.401 14178 Z= 0.294 Chirality : 0.047 0.160 1572 Planarity : 0.005 0.043 1844 Dihedral : 7.691 106.669 1514 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1294 helix: 1.09 (0.27), residues: 400 sheet: -0.34 (0.37), residues: 220 loop : -0.64 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 125 HIS 0.003 0.001 HIS B 390 PHE 0.013 0.001 PHE B 486 TYR 0.013 0.001 TYR A 491 ARG 0.002 0.000 ARG A 447 *********************** 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 48 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.101 Fit side-chains REVERT: B 179 ASP cc_start: 0.6413 (t0) cc_final: 0.6192 (t0) REVERT: B 402 GLU cc_start: 0.8361 (mp0) cc_final: 0.8079 (mp0) REVERT: B 566 GLU cc_start: 0.5897 (tp30) cc_final: 0.5659 (pt0) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2089 time to fit residues: 15.9970 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 : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 36 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 59 optimal weight: 0.1980 chunk 4 optimal weight: 0.0170 chunk 70 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 38 optimal weight: 0.0970 chunk 71 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 overall best weight: 2.2620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN B 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.053465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.039271 restraints weight = 30767.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.040668 restraints weight = 18303.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.041584 restraints weight = 13165.297| |-----------------------------------------------------------------------------| r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10380 Z= 0.163 Angle : 0.539 8.103 14178 Z= 0.272 Chirality : 0.046 0.158 1572 Planarity : 0.004 0.041 1844 Dihedral : 7.051 106.419 1514 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1294 helix: 1.18 (0.27), residues: 400 sheet: -0.09 (0.39), residues: 202 loop : -0.72 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 668 HIS 0.003 0.001 HIS A 144 PHE 0.013 0.001 PHE A 477 TYR 0.012 0.001 TYR A 367 ARG 0.004 0.000 ARG B 156 *********************** 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 54 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 1.216 Fit side-chains REVERT: B 179 ASP cc_start: 0.6435 (t0) cc_final: 0.6210 (t0) REVERT: B 402 GLU cc_start: 0.8343 (mp0) cc_final: 0.8063 (mp0) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.2028 time to fit residues: 17.5020 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 : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 43 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.051554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.037627 restraints weight = 31346.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.038980 restraints weight = 18842.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.039812 restraints weight = 13576.151| |-----------------------------------------------------------------------------| r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1323 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= 0.295 Angle : 0.615 12.348 14178 Z= 0.310 Chirality : 0.048 0.167 1572 Planarity : 0.005 0.043 1844 Dihedral : 6.805 103.644 1514 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1294 helix: 1.00 (0.26), residues: 400 sheet: -0.70 (0.36), residues: 222 loop : -0.70 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 125 HIS 0.003 0.001 HIS B 390 PHE 0.016 0.002 PHE A 477 TYR 0.015 0.002 TYR A 367 ARG 0.004 0.000 ARG B 156 *********************** 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 : 1.070 Fit side-chains REVERT: B 146 MET cc_start: 0.6676 (mtp) cc_final: 0.6313 (mtp) REVERT: B 402 GLU cc_start: 0.8403 (mp0) cc_final: 0.8091 (mp0) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.2116 time to fit residues: 15.5919 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 : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 114 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 61 optimal weight: 0.1980 chunk 33 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.2803 r_free = 0.2803 target = 0.053391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.039173 restraints weight = 30617.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.040561 restraints weight = 18293.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.041463 restraints weight = 13222.599| |-----------------------------------------------------------------------------| r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10380 Z= 0.158 Angle : 0.541 9.130 14178 Z= 0.272 Chirality : 0.046 0.148 1572 Planarity : 0.005 0.040 1844 Dihedral : 6.517 104.904 1514 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.24), residues: 1294 helix: 1.16 (0.26), residues: 400 sheet: -0.57 (0.37), residues: 220 loop : -0.68 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 125 HIS 0.002 0.000 HIS B 92 PHE 0.018 0.001 PHE B 365 TYR 0.010 0.001 TYR A 491 ARG 0.003 0.000 ARG B 156 *********************** 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 50 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2268 time to fit residues: 17.2162 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 : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 88 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 = 0.2756 r_free = 0.2756 target = 0.051107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.037540 restraints weight = 31261.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.038811 restraints weight = 18983.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.039729 restraints weight = 13950.422| |-----------------------------------------------------------------------------| r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10380 Z= 0.311 Angle : 0.626 12.536 14178 Z= 0.314 Chirality : 0.049 0.167 1572 Planarity : 0.005 0.043 1844 Dihedral : 6.746 104.657 1514 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1294 helix: 0.96 (0.26), residues: 400 sheet: -0.84 (0.36), residues: 220 loop : -0.80 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 125 HIS 0.004 0.001 HIS A 144 PHE 0.027 0.002 PHE A 486 TYR 0.014 0.002 TYR A 491 ARG 0.004 0.000 ARG B 156 *********************** 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 43 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 1.134 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.2018 time to fit residues: 14.0946 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 : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 20 optimal weight: 0.5980 chunk 83 optimal weight: 0.2980 chunk 58 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.2801 r_free = 0.2801 target = 0.053224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.039141 restraints weight = 31016.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.040525 restraints weight = 18554.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.041471 restraints weight = 13360.547| |-----------------------------------------------------------------------------| r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10380 Z= 0.148 Angle : 0.545 9.212 14178 Z= 0.273 Chirality : 0.046 0.145 1572 Planarity : 0.005 0.041 1844 Dihedral : 6.470 106.476 1514 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1294 helix: 1.17 (0.27), residues: 400 sheet: -0.69 (0.37), residues: 222 loop : -0.68 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 590 HIS 0.002 0.000 HIS B 92 PHE 0.019 0.001 PHE A 486 TYR 0.010 0.001 TYR A 74 ARG 0.002 0.000 ARG A 447 *********************** 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 50 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.128 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2188 time to fit residues: 16.7402 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 : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 104 optimal weight: 0.0870 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 20.0000 chunk 57 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 overall best weight: 4.7364 ------------------------------------------------------------------------------- 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 = 0.2782 r_free = 0.2782 target = 0.052261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.038232 restraints weight = 31644.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.039567 restraints weight = 18959.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.040487 restraints weight = 13734.086| |-----------------------------------------------------------------------------| r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1493 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= 0.248 Angle : 0.588 11.064 14178 Z= 0.295 Chirality : 0.047 0.160 1572 Planarity : 0.005 0.045 1844 Dihedral : 6.556 106.137 1514 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.24), residues: 1294 helix: 1.05 (0.27), residues: 400 sheet: -0.77 (0.37), residues: 222 loop : -0.73 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.003 0.001 HIS A 591 PHE 0.023 0.002 PHE A 486 TYR 0.017 0.001 TYR B 177 ARG 0.003 0.000 ARG B 156 *********************** 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 48 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.281 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2065 time to fit residues: 15.9358 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 : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.052305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.038266 restraints weight = 31195.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.039659 restraints weight = 18569.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.040560 restraints weight = 13322.072| |-----------------------------------------------------------------------------| r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1560 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= 0.243 Angle : 0.596 11.303 14178 Z= 0.298 Chirality : 0.048 0.169 1572 Planarity : 0.005 0.045 1844 Dihedral : 6.602 107.929 1514 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.24), residues: 1294 helix: 0.95 (0.26), residues: 400 sheet: -0.80 (0.37), residues: 222 loop : -0.75 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 125 HIS 0.003 0.001 HIS A 144 PHE 0.022 0.002 PHE A 486 TYR 0.017 0.001 TYR A 367 ARG 0.003 0.000 ARG A 447 *********************** 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 47 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.214 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2080 time to fit residues: 15.6687 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 : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 121 optimal weight: 30.0000 chunk 125 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.052061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.037979 restraints weight = 31453.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.039350 restraints weight = 18859.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.040243 restraints weight = 13594.804| |-----------------------------------------------------------------------------| r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1580 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= 0.241 Angle : 0.594 11.419 14178 Z= 0.297 Chirality : 0.048 0.185 1572 Planarity : 0.005 0.045 1844 Dihedral : 6.603 109.469 1514 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1294 helix: 0.94 (0.26), residues: 400 sheet: -0.80 (0.36), residues: 222 loop : -0.76 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.003 0.001 HIS A 144 PHE 0.022 0.002 PHE A 486 TYR 0.014 0.001 TYR A 367 ARG 0.003 0.000 ARG A 447 ********************** 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 46 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.136 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2048 time to fit residues: 15.0895 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 : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 51 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.2788 r_free = 0.2788 target = 0.052506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.038566 restraints weight = 31072.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.039925 restraints weight = 18730.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.040802 restraints weight = 13573.481| |-----------------------------------------------------------------------------| r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10380 Z= 0.211 Angle : 0.581 10.861 14178 Z= 0.291 Chirality : 0.047 0.166 1572 Planarity : 0.005 0.045 1844 Dihedral : 6.554 110.424 1514 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1294 helix: 0.96 (0.26), residues: 400 sheet: -0.73 (0.37), residues: 222 loop : -0.72 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.002 0.001 HIS B 92 PHE 0.021 0.001 PHE A 486 TYR 0.014 0.001 TYR A 367 ARG 0.003 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2630.89 seconds wall clock time: 49 minutes 8.93 seconds (2948.93 seconds total)