Starting phenix.real_space_refine on Thu May 1 03:02:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ors_17131/05_2025/8ors_17131.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ors_17131/05_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_17131/05_2025/8ors_17131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ors_17131/05_2025/8ors_17131.map" model { file = "/net/cci-nas-00/data/ceres_data/8ors_17131/05_2025/8ors_17131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ors_17131/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 8.47, per 1000 atoms: 0.84 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: 2.82 Conformation dependent library (CDL) restraints added in 1.3 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: 1.23 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: 3.61 Time building geometry restraints manager: 2.94 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.330 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: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.030 ------------------------------------------------------------------------------- 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 : 7.43 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 Details of bonding type rmsd hydrogen bonds : bond 0.22776 ( 367) hydrogen bonds : angle 8.04280 ( 1056) covalent geometry : bond 0.00327 (10380) covalent geometry : angle 0.55110 (14178) *********************** 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 : 1.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2357 time to fit residues: 17.4100 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 : 1.056 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.038542 restraints weight = 31063.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.039934 restraints weight = 18451.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.040870 restraints weight = 13204.832| |-----------------------------------------------------------------------------| r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 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= 0.144 Angle : 0.576 9.403 14178 Z= 0.294 Chirality : 0.047 0.160 1572 Planarity : 0.005 0.043 1844 Dihedral : 7.691 106.667 1514 Min Nonbonded Distance : 2.477 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 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 367) hydrogen bonds : angle 5.46292 ( 1056) covalent geometry : bond 0.00333 (10380) covalent geometry : angle 0.57592 (14178) *********************** 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 : 1.539 Fit side-chains REVERT: B 179 ASP cc_start: 0.6454 (t0) cc_final: 0.6229 (t0) REVERT: B 402 GLU cc_start: 0.8365 (mp0) cc_final: 0.8082 (mp0) REVERT: B 566 GLU cc_start: 0.5882 (tp30) cc_final: 0.5629 (pt0) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1917 time to fit residues: 14.8450 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 : 1.120 ------------------------------------------------------------------------------- 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: 1.9990 chunk 121 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 59 optimal weight: 0.0270 chunk 4 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 overall best weight: 3.3644 ------------------------------------------------------------------------------- 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 = 0.2795 r_free = 0.2795 target = 0.052817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.038675 restraints weight = 31173.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.040050 restraints weight = 18593.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.040966 restraints weight = 13441.800| |-----------------------------------------------------------------------------| r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10380 Z= 0.129 Angle : 0.561 9.158 14178 Z= 0.283 Chirality : 0.046 0.162 1572 Planarity : 0.005 0.041 1844 Dihedral : 7.108 106.170 1514 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.09 % Allowed : 2.59 % Favored : 97.32 % 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: -0.14 (0.24), residues: 1294 helix: 1.10 (0.26), residues: 400 sheet: -0.19 (0.38), residues: 202 loop : -0.75 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 125 HIS 0.003 0.001 HIS A 144 PHE 0.015 0.001 PHE A 486 TYR 0.013 0.001 TYR A 367 ARG 0.005 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 367) hydrogen bonds : angle 5.20401 ( 1056) covalent geometry : bond 0.00303 (10380) covalent geometry : angle 0.56080 (14178) *********************** 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 50 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 1.468 Fit side-chains REVERT: B 402 GLU cc_start: 0.8344 (mp0) cc_final: 0.8064 (mp0) outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 0.2646 time to fit residues: 21.6729 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 : 1.113 ------------------------------------------------------------------------------- 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: 20.0000 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.2770 r_free = 0.2770 target = 0.051673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.037668 restraints weight = 31299.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.039016 restraints weight = 18741.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.039832 restraints weight = 13538.794| |-----------------------------------------------------------------------------| r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10380 Z= 0.182 Angle : 0.607 11.888 14178 Z= 0.306 Chirality : 0.048 0.170 1572 Planarity : 0.005 0.043 1844 Dihedral : 6.814 103.448 1514 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % 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: 0.97 (0.26), residues: 400 sheet: -0.71 (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 0.024 0.002 PHE A 486 TYR 0.015 0.001 TYR A 367 ARG 0.003 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 367) hydrogen bonds : angle 5.16752 ( 1056) covalent geometry : bond 0.00434 (10380) covalent geometry : angle 0.60666 (14178) *********************** 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 48 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 2.057 Fit side-chains REVERT: B 146 MET cc_start: 0.6683 (mtp) cc_final: 0.6328 (mtp) REVERT: B 179 ASP cc_start: 0.6558 (t0) cc_final: 0.6246 (t0) REVERT: B 402 GLU cc_start: 0.8401 (mp0) cc_final: 0.8110 (mp0) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.3044 time to fit residues: 22.4609 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 : 1.292 ------------------------------------------------------------------------------- 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: 20.0000 chunk 20 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 chunk 33 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.8824 ------------------------------------------------------------------------------- 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 = 0.2791 r_free = 0.2791 target = 0.052807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.038811 restraints weight = 30833.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.040205 restraints weight = 18424.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.041105 restraints weight = 13235.457| |-----------------------------------------------------------------------------| r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1329 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= 0.116 Angle : 0.553 9.642 14178 Z= 0.278 Chirality : 0.046 0.154 1572 Planarity : 0.005 0.042 1844 Dihedral : 6.574 104.459 1514 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -0.22 (0.24), residues: 1294 helix: 1.09 (0.26), residues: 400 sheet: -0.59 (0.37), residues: 220 loop : -0.70 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.002 0.000 HIS A 591 PHE 0.022 0.001 PHE B 365 TYR 0.011 0.001 TYR A 491 ARG 0.003 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 367) hydrogen bonds : angle 4.94232 ( 1056) covalent geometry : bond 0.00269 (10380) covalent geometry : angle 0.55281 (14178) *********************** 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 : 1.090 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2345 time to fit residues: 18.4368 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 : 1.191 ------------------------------------------------------------------------------- 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: 9.9990 chunk 102 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 overall best weight: 7.1788 ------------------------------------------------------------------------------- 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 = 0.2745 r_free = 0.2745 target = 0.050636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.037306 restraints weight = 31414.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.038609 restraints weight = 19235.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.039423 restraints weight = 14005.414| |-----------------------------------------------------------------------------| r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10380 Z= 0.225 Angle : 0.652 13.167 14178 Z= 0.327 Chirality : 0.050 0.171 1572 Planarity : 0.005 0.044 1844 Dihedral : 6.851 103.846 1514 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.55 (0.24), residues: 1294 helix: 0.81 (0.26), residues: 402 sheet: -0.95 (0.36), residues: 220 loop : -0.84 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 125 HIS 0.005 0.001 HIS A 144 PHE 0.020 0.002 PHE A 486 TYR 0.015 0.002 TYR A 491 ARG 0.003 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.04806 ( 367) hydrogen bonds : angle 5.14594 ( 1056) covalent geometry : bond 0.00534 (10380) covalent geometry : angle 0.65151 (14178) *********************** 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 42 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.244 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2026 time to fit residues: 13.7706 Evaluate side-chains 34 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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: 8.9990 chunk 83 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 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 = 0.2767 r_free = 0.2767 target = 0.051636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.038059 restraints weight = 31215.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.039398 restraints weight = 18977.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.040287 restraints weight = 13747.752| |-----------------------------------------------------------------------------| r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1515 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= 0.156 Angle : 0.601 11.854 14178 Z= 0.302 Chirality : 0.047 0.159 1572 Planarity : 0.005 0.043 1844 Dihedral : 6.726 105.091 1514 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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: -0.48 (0.24), residues: 1294 helix: 0.92 (0.26), residues: 400 sheet: -0.97 (0.36), residues: 222 loop : -0.80 (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 591 PHE 0.021 0.002 PHE A 593 TYR 0.013 0.001 TYR A 491 ARG 0.003 0.000 ARG A 637 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 367) hydrogen bonds : angle 5.01688 ( 1056) covalent geometry : bond 0.00368 (10380) covalent geometry : angle 0.60118 (14178) *********************** 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 46 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.156 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2234 time to fit residues: 15.9667 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 : 1.158 ------------------------------------------------------------------------------- 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: 0.0970 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 57 optimal weight: 0.0570 chunk 22 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 overall best weight: 0.8900 ------------------------------------------------------------------------------- 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 = 0.2824 r_free = 0.2824 target = 0.054253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.039976 restraints weight = 30581.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.041413 restraints weight = 18067.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.042329 restraints weight = 12905.585| |-----------------------------------------------------------------------------| r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1495 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= 0.093 Angle : 0.539 7.739 14178 Z= 0.269 Chirality : 0.046 0.139 1572 Planarity : 0.005 0.043 1844 Dihedral : 6.402 106.700 1514 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -0.14 (0.24), residues: 1294 helix: 1.20 (0.27), residues: 400 sheet: -0.65 (0.37), residues: 222 loop : -0.65 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 590 HIS 0.002 0.000 HIS A 73 PHE 0.015 0.001 PHE A 477 TYR 0.011 0.001 TYR B 74 ARG 0.002 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 367) hydrogen bonds : angle 4.76335 ( 1056) covalent geometry : bond 0.00202 (10380) covalent geometry : angle 0.53918 (14178) *********************** 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 52 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1892 time to fit residues: 15.7677 Evaluate side-chains 40 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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: 5.9990 chunk 126 optimal weight: 10.0000 chunk 17 optimal weight: 0.0060 chunk 97 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 overall best weight: 4.0004 ------------------------------------------------------------------------------- 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 = 0.2789 r_free = 0.2789 target = 0.052536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.038517 restraints weight = 31214.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.039902 restraints weight = 18694.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.040811 restraints weight = 13405.123| |-----------------------------------------------------------------------------| r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10380 Z= 0.139 Angle : 0.573 10.319 14178 Z= 0.286 Chirality : 0.047 0.157 1572 Planarity : 0.005 0.045 1844 Dihedral : 6.444 105.584 1514 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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 (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: -0.26 (0.24), residues: 1294 helix: 1.08 (0.26), residues: 400 sheet: -0.76 (0.37), residues: 222 loop : -0.69 (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 0.015 0.001 PHE A 477 TYR 0.016 0.001 TYR B 177 ARG 0.003 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 367) hydrogen bonds : angle 4.81586 ( 1056) covalent geometry : bond 0.00329 (10380) covalent geometry : angle 0.57290 (14178) *********************** 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 : 1.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2196 time to fit residues: 16.1814 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 : 1.044 ------------------------------------------------------------------------------- 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: 20.0000 chunk 125 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 30.0000 chunk 5 optimal weight: 0.0980 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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 = 0.2794 r_free = 0.2794 target = 0.052787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.038928 restraints weight = 31108.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.040256 restraints weight = 18882.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.041161 restraints weight = 13744.163| |-----------------------------------------------------------------------------| r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10380 Z= 0.127 Angle : 0.566 10.018 14178 Z= 0.283 Chirality : 0.047 0.166 1572 Planarity : 0.005 0.045 1844 Dihedral : 6.437 107.181 1514 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % 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: -0.27 (0.24), residues: 1294 helix: 1.05 (0.26), residues: 400 sheet: -0.72 (0.37), residues: 222 loop : -0.70 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 125 HIS 0.002 0.001 HIS B 92 PHE 0.018 0.001 PHE B 184 TYR 0.014 0.001 TYR B 177 ARG 0.003 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 367) hydrogen bonds : angle 4.80792 ( 1056) covalent geometry : bond 0.00298 (10380) covalent geometry : angle 0.56584 (14178) ********************** 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 47 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.054 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1906 time to fit residues: 14.3509 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 : 1.045 ------------------------------------------------------------------------------- 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: 3.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 75 optimal weight: 0.0670 chunk 106 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- 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 = 0.2791 r_free = 0.2791 target = 0.052605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.038586 restraints weight = 31138.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.039977 restraints weight = 18581.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.040890 restraints weight = 13339.446| |-----------------------------------------------------------------------------| r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1571 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= 0.136 Angle : 0.575 10.411 14178 Z= 0.287 Chirality : 0.047 0.156 1572 Planarity : 0.005 0.045 1844 Dihedral : 6.465 107.744 1514 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % 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: -0.32 (0.24), residues: 1294 helix: 0.98 (0.26), residues: 400 sheet: -0.73 (0.37), residues: 222 loop : -0.71 (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 A 144 PHE 0.018 0.001 PHE B 184 TYR 0.012 0.001 TYR B 177 ARG 0.003 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 367) hydrogen bonds : angle 4.81745 ( 1056) covalent geometry : bond 0.00322 (10380) covalent geometry : angle 0.57502 (14178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3106.16 seconds wall clock time: 57 minutes 2.63 seconds (3422.63 seconds total)