Starting phenix.real_space_refine on Wed Aug 5 21:01:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9g_65774/08_2026/9w9g_65774.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9g_65774/08_2026/9w9g_65774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w9g_65774/08_2026/9w9g_65774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9g_65774/08_2026/9w9g_65774.map" model { file = "/net/cci-nas-00/data/ceres_data/9w9g_65774/08_2026/9w9g_65774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9g_65774/08_2026/9w9g_65774.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 75 5.49 5 S 37 5.16 5 C 6930 2.51 5 N 2039 2.21 5 O 2361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11442 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 7152 Classifications: {'peptide': 889} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 836} Chain: "B" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2696 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 23, 'TRANS': 312} Chain: "R" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1594 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 35} Link IDs: {'rna2p': 11, 'rna3p': 63} Time building chain proxies: 2.13, per 1000 atoms: 0.19 Number of scatterers: 11442 At special positions: 0 Unit cell: (119.52, 99.6, 118.413, 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 37 16.00 P 75 15.00 O 2361 8.00 N 2039 7.00 C 6930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 358.1 milliseconds 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 43.3% alpha, 16.2% beta 21 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 59 through 73 removed outlier: 4.194A pdb=" N ALA A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 99 Processing helix chain 'A' and resid 104 through 111 removed outlier: 3.869A pdb=" N TYR A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 191 Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 247 through 253 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.595A pdb=" N ARG A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 299 Processing helix chain 'A' and resid 336 through 345 Processing helix chain 'A' and resid 384 through 407 removed outlier: 3.958A pdb=" N MET A 388 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 removed outlier: 3.556A pdb=" N ILE A 411 " --> pdb=" O TYR A 407 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 445 Processing helix chain 'A' and resid 461 through 477 Processing helix chain 'A' and resid 526 through 538 Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.626A pdb=" N ALA A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 606 Processing helix chain 'A' and resid 610 through 615 Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 629 through 638 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 710 through 721 Processing helix chain 'A' and resid 744 through 757 removed outlier: 3.531A pdb=" N ARG A 749 " --> pdb=" O GLY A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 788 removed outlier: 3.632A pdb=" N LYS A 777 " --> pdb=" O ASP A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 806 No H-bonds generated for 'chain 'A' and resid 804 through 806' Processing helix chain 'A' and resid 849 through 865 Processing helix chain 'A' and resid 889 through 906 removed outlier: 3.677A pdb=" N MET A 893 " --> pdb=" O ALA A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 917 removed outlier: 3.701A pdb=" N GLU A 912 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE A 913 " --> pdb=" O ARG A 909 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 914 " --> pdb=" O LYS A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 945 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 268 through 275 removed outlier: 3.510A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 300 Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 385 through 407 removed outlier: 3.977A pdb=" N LEU B 389 " --> pdb=" O TYR B 385 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 418 removed outlier: 3.540A pdb=" N ILE B 411 " --> pdb=" O TYR B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 444 Processing helix chain 'B' and resid 461 through 477 Processing helix chain 'B' and resid 526 through 538 Processing helix chain 'B' and resid 540 through 543 Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 565 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 155 removed outlier: 6.396A pdb=" N VAL A 162 " --> pdb=" O HIS A 149 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE A 151 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE A 160 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARG A 153 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A 158 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 205 Processing sheet with id=AA3, first strand: chain 'A' and resid 302 through 303 removed outlier: 6.450A pdb=" N ILE A 302 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE A 354 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N HIS A 558 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 564 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE A 517 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A 510 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER A 519 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE A 508 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 432 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 310 removed outlier: 4.312A pdb=" N GLN B 322 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 651 through 654 removed outlier: 5.044A pdb=" N SER A 663 " --> pdb=" O PRO A 675 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA A 672 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU A 707 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE A 674 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N CYS A 709 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TYR A 925 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N HIS A 920 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU A 732 " --> pdb=" O HIS A 920 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU A 922 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA A 730 " --> pdb=" O GLU A 922 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU A 924 " --> pdb=" O CYS A 728 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N CYS A 728 " --> pdb=" O LEU A 924 " (cutoff:3.500A) removed outlier: 15.179A pdb=" N ARG A 724 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 14.751A pdb=" N LEU A 880 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 14.283A pdb=" N LEU A 726 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 12.191A pdb=" N ALA A 878 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N CYS A 728 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ALA A 876 " --> pdb=" O CYS A 728 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A 730 " --> pdb=" O ALA A 874 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA A 874 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU A 732 " --> pdb=" O PHE A 872 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLY A 873 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N TYR A 839 " --> pdb=" O GLY A 873 " (cutoff:3.500A) removed outlier: 15.298A pdb=" N GLY A 875 " --> pdb=" O TYR A 839 " (cutoff:3.500A) removed outlier: 19.068A pdb=" N PHE A 841 " --> pdb=" O GLY A 875 " (cutoff:3.500A) removed outlier: 23.670A pdb=" N THR A 877 " --> pdb=" O PHE A 841 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL A 837 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA A 827 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 822 " --> pdb=" O ALA A 813 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 302 through 303 removed outlier: 6.289A pdb=" N ILE B 302 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR B 372 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 302 through 303 removed outlier: 6.289A pdb=" N ILE B 302 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N HIS B 558 " --> pdb=" O ARG B 523 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 517 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 510 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER B 519 " --> pdb=" O PHE B 508 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHE B 508 " --> pdb=" O SER B 519 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 309 through 310 448 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2996 1.33 - 1.45: 2552 1.45 - 1.57: 6096 1.57 - 1.69: 149 1.69 - 1.81: 67 Bond restraints: 11860 Sorted by residual: bond pdb=" N VAL A 424 " pdb=" CA VAL A 424 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.17e-02 7.31e+03 1.01e+01 bond pdb=" N ILE A 512 " pdb=" CA ILE A 512 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.18e-02 7.18e+03 9.01e+00 bond pdb=" N VAL A 423 " pdb=" CA VAL A 423 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.30e-02 5.92e+03 8.37e+00 bond pdb=" N TYR A 481 " pdb=" CA TYR A 481 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.24e-02 6.50e+03 7.56e+00 bond pdb=" P U R 64 " pdb=" O5' U R 64 " ideal model delta sigma weight residual 1.593 1.620 -0.027 1.00e-02 1.00e+04 7.26e+00 ... (remaining 11855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 15509 1.40 - 2.79: 724 2.79 - 4.19: 140 4.19 - 5.59: 27 5.59 - 6.98: 11 Bond angle restraints: 16411 Sorted by residual: angle pdb=" N ASP A 479 " pdb=" CA ASP A 479 " pdb=" C ASP A 479 " ideal model delta sigma weight residual 113.18 108.04 5.14 1.21e+00 6.83e-01 1.80e+01 angle pdb=" N1 C R 61 " pdb=" C2 C R 61 " pdb=" O2 C R 61 " ideal model delta sigma weight residual 118.90 121.31 -2.41 6.00e-01 2.78e+00 1.61e+01 angle pdb=" N9 A R 50 " pdb=" C4 A R 50 " pdb=" C5 A R 50 " ideal model delta sigma weight residual 105.80 104.31 1.49 4.00e-01 6.25e+00 1.40e+01 angle pdb=" O5' C R 49 " pdb=" C5' C R 49 " pdb=" C4' C R 49 " ideal model delta sigma weight residual 109.40 112.24 -2.84 8.00e-01 1.56e+00 1.26e+01 angle pdb=" CA VAL A 423 " pdb=" C VAL A 423 " pdb=" O VAL A 423 " ideal model delta sigma weight residual 121.58 118.10 3.48 1.00e+00 1.00e+00 1.21e+01 ... (remaining 16406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.48: 6843 27.48 - 54.96: 316 54.96 - 82.44: 165 82.44 - 109.92: 3 109.92 - 137.39: 2 Dihedral angle restraints: 7329 sinusoidal: 3779 harmonic: 3550 Sorted by residual: dihedral pdb=" O4' U R 60 " pdb=" C1' U R 60 " pdb=" N1 U R 60 " pdb=" C2 U R 60 " ideal model delta sinusoidal sigma weight residual -128.00 -67.69 -60.31 1 1.70e+01 3.46e-03 1.68e+01 dihedral pdb=" CA ILE A 344 " pdb=" C ILE A 344 " pdb=" N ALA A 345 " pdb=" CA ALA A 345 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" C4' C R 48 " pdb=" C3' C R 48 " pdb=" O3' C R 48 " pdb=" P C R 49 " ideal model delta sinusoidal sigma weight residual -110.00 18.69 -128.69 1 3.50e+01 8.16e-04 1.27e+01 ... (remaining 7326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1674 0.105 - 0.209: 140 0.209 - 0.313: 1 0.313 - 0.418: 0 0.418 - 0.522: 8 Chirality restraints: 1823 Sorted by residual: chirality pdb=" P U R 64 " pdb=" OP1 U R 64 " pdb=" OP2 U R 64 " pdb=" O5' U R 64 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" P U R 20 " pdb=" OP1 U R 20 " pdb=" OP2 U R 20 " pdb=" O5' U R 20 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.20e+00 chirality pdb=" P G R 52 " pdb=" OP1 G R 52 " pdb=" OP2 G R 52 " pdb=" O5' G R 52 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 5.97e+00 ... (remaining 1820 not shown) Planarity restraints: 1885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 446 " -0.011 2.00e-02 2.50e+03 1.35e-02 4.57e+00 pdb=" CG TRP A 446 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 446 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 446 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 446 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 446 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 446 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 446 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 446 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 446 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 690 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" C THR A 690 " 0.035 2.00e-02 2.50e+03 pdb=" O THR A 690 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN A 691 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 166 " 0.159 9.50e-02 1.11e+02 7.16e-02 3.98e+00 pdb=" NE ARG A 166 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 166 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 166 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 166 " 0.000 2.00e-02 2.50e+03 ... (remaining 1882 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 4576 2.92 - 3.41: 11862 3.41 - 3.91: 21495 3.91 - 4.40: 24140 4.40 - 4.90: 36088 Nonbonded interactions: 98161 Sorted by model distance: nonbonded pdb=" O VAL A 424 " pdb=" N ASP A 479 " model vdw 2.420 3.120 nonbonded pdb=" O MET A 696 " pdb=" N LYS A 701 " model vdw 2.467 3.120 nonbonded pdb=" O2' U R 20 " pdb=" O5' C R 20A" model vdw 2.497 3.040 nonbonded pdb=" O GLU A 421 " pdb=" NH2 ARG A 513 " model vdw 2.508 3.120 nonbonded pdb=" O PRO A 711 " pdb=" OG SER A 715 " model vdw 2.529 3.040 ... (remaining 98156 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.560 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 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 : 0.004 0.041 11860 Z= 0.223 Angle : 0.702 6.983 16411 Z= 0.447 Chirality : 0.059 0.522 1823 Planarity : 0.005 0.072 1885 Dihedral : 17.094 137.395 5037 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.57 % Allowed : 8.57 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.24), residues: 1221 helix: 1.33 (0.23), residues: 487 sheet: -0.52 (0.36), residues: 206 loop : 0.25 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 166 TYR 0.023 0.002 TYR A 685 PHE 0.023 0.002 PHE A 292 TRP 0.036 0.002 TRP A 446 HIS 0.003 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.22 (11860) covalent geometry : angle 0.70226 / 0.45 (16411) hydrogen bonds : bond 0.11248 / 7.62 ( 499) hydrogen bonds : angle 6.64197 / 4.97 ( 1368) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 225 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 ASN cc_start: 0.7912 (t0) cc_final: 0.7121 (m-40) REVERT: A 504 PHE cc_start: 0.6836 (m-80) cc_final: 0.6558 (m-80) REVERT: A 709 CYS cc_start: -0.6357 (p) cc_final: -0.6722 (p) REVERT: B 341 GLN cc_start: 0.8035 (mt0) cc_final: 0.7502 (mt0) REVERT: B 529 MET cc_start: 0.8398 (tpt) cc_final: 0.7723 (tpt) outliers start: 6 outliers final: 3 residues processed: 230 average time/residue: 0.1190 time to fit residues: 36.2881 Evaluate side-chains 139 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 124 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 HIS A 205 GLN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN A 691 GLN A 739 ASN A 860 GLN B 341 GLN ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.150354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.116256 restraints weight = 47760.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.113754 restraints weight = 35859.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.114772 restraints weight = 26470.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.115815 restraints weight = 21777.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.116777 restraints weight = 17983.634| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11860 Z= 0.219 Angle : 0.721 13.328 16411 Z= 0.378 Chirality : 0.045 0.256 1823 Planarity : 0.006 0.088 1885 Dihedral : 18.236 132.664 2569 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.52 % Allowed : 12.10 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.24), residues: 1221 helix: 0.98 (0.23), residues: 492 sheet: -0.85 (0.36), residues: 201 loop : 0.24 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 269 TYR 0.038 0.003 TYR B 547 PHE 0.029 0.003 PHE B 292 TRP 0.026 0.003 TRP A 653 HIS 0.010 0.001 HIS A 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (11860) covalent geometry : angle 0.72119 / 0.38 (16411) hydrogen bonds : bond 0.05562 / 3.71 ( 499) hydrogen bonds : angle 5.89186 / 4.39 ( 1368) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7655 (mm-30) REVERT: A 107 MET cc_start: 0.7309 (mtp) cc_final: 0.6711 (mtt) REVERT: A 153 ARG cc_start: 0.5070 (OUTLIER) cc_final: 0.4760 (ptm-80) REVERT: A 324 ASN cc_start: 0.7946 (t0) cc_final: 0.7330 (m-40) REVERT: A 381 ILE cc_start: 0.6074 (mm) cc_final: 0.5590 (mm) REVERT: A 419 PRO cc_start: 0.8018 (Cg_endo) cc_final: 0.7514 (Cg_exo) REVERT: A 496 MET cc_start: 0.7053 (tpp) cc_final: 0.6503 (tpp) REVERT: A 709 CYS cc_start: -0.5866 (p) cc_final: -0.6181 (p) REVERT: A 732 GLU cc_start: 0.6071 (mt-10) cc_final: 0.5728 (tp30) REVERT: B 341 GLN cc_start: 0.8349 (mt0) cc_final: 0.8121 (mt0) REVERT: B 388 MET cc_start: 0.8490 (tmm) cc_final: 0.8176 (ttt) REVERT: B 529 MET cc_start: 0.8904 (tpt) cc_final: 0.8648 (tpp) outliers start: 37 outliers final: 19 residues processed: 161 average time/residue: 0.1091 time to fit residues: 24.6614 Evaluate side-chains 133 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 720 LYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain B residue 546 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 61 optimal weight: 7.9990 chunk 73 optimal weight: 0.0060 chunk 57 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 290 ASN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.147272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.112188 restraints weight = 49124.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.110602 restraints weight = 38095.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.111446 restraints weight = 28103.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.112379 restraints weight = 22971.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.113308 restraints weight = 19265.336| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11860 Z= 0.202 Angle : 0.672 8.413 16411 Z= 0.354 Chirality : 0.043 0.299 1823 Planarity : 0.006 0.074 1885 Dihedral : 18.325 129.243 2566 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.76 % Allowed : 14.38 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1221 helix: 0.98 (0.23), residues: 491 sheet: -0.66 (0.37), residues: 183 loop : 0.05 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 359 TYR 0.032 0.002 TYR B 481 PHE 0.026 0.003 PHE B 292 TRP 0.014 0.002 TRP A 653 HIS 0.005 0.001 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (11860) covalent geometry : angle 0.67193 / 0.35 (16411) hydrogen bonds : bond 0.05363 / 3.56 ( 499) hydrogen bonds : angle 5.66333 / 4.20 ( 1368) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7567 (mm-30) REVERT: A 107 MET cc_start: 0.7391 (mtp) cc_final: 0.6788 (mtt) REVERT: A 153 ARG cc_start: 0.4997 (OUTLIER) cc_final: 0.4762 (ptm-80) REVERT: A 257 ARG cc_start: 0.6166 (mpt180) cc_final: 0.5660 (mmt-90) REVERT: A 322 GLN cc_start: 0.5710 (OUTLIER) cc_final: 0.5362 (mm-40) REVERT: A 324 ASN cc_start: 0.8081 (t0) cc_final: 0.7448 (m-40) REVERT: A 342 MET cc_start: 0.6639 (mpp) cc_final: 0.6396 (mpp) REVERT: A 523 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6970 (mmm-85) REVERT: A 709 CYS cc_start: -0.5949 (p) cc_final: -0.6341 (p) REVERT: A 732 GLU cc_start: 0.6027 (mt-10) cc_final: 0.5612 (tp30) REVERT: B 341 GLN cc_start: 0.8464 (mt0) cc_final: 0.8180 (mt0) REVERT: B 388 MET cc_start: 0.8452 (tmm) cc_final: 0.7951 (ttt) REVERT: B 529 MET cc_start: 0.8956 (tpt) cc_final: 0.8644 (tpp) REVERT: B 547 TYR cc_start: 0.8214 (t80) cc_final: 0.7686 (t80) outliers start: 29 outliers final: 19 residues processed: 140 average time/residue: 0.1111 time to fit residues: 21.5071 Evaluate side-chains 127 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain B residue 546 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 7 optimal weight: 7.9990 chunk 123 optimal weight: 40.0000 chunk 50 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 GLN ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.143499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.109361 restraints weight = 50524.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.107421 restraints weight = 38630.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.108440 restraints weight = 27855.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.109406 restraints weight = 22555.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.110258 restraints weight = 19232.374| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11860 Z= 0.228 Angle : 0.692 9.660 16411 Z= 0.370 Chirality : 0.045 0.298 1823 Planarity : 0.006 0.085 1885 Dihedral : 18.502 129.589 2566 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.14 % Allowed : 15.62 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.24), residues: 1221 helix: 0.80 (0.23), residues: 484 sheet: -0.81 (0.37), residues: 181 loop : -0.05 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 359 TYR 0.030 0.002 TYR B 481 PHE 0.028 0.003 PHE B 292 TRP 0.028 0.002 TRP A 653 HIS 0.007 0.001 HIS A 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 (11860) covalent geometry : angle 0.69180 / 0.37 (16411) hydrogen bonds : bond 0.05363 / 3.55 ( 499) hydrogen bonds : angle 5.63218 / 4.17 ( 1368) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7554 (mm-30) REVERT: A 107 MET cc_start: 0.7483 (mtp) cc_final: 0.6879 (mtt) REVERT: A 124 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.5564 (ppt170) REVERT: A 297 ASP cc_start: 0.8123 (m-30) cc_final: 0.7749 (m-30) REVERT: A 322 GLN cc_start: 0.5964 (OUTLIER) cc_final: 0.5537 (mm-40) REVERT: A 324 ASN cc_start: 0.8065 (t0) cc_final: 0.7213 (m-40) REVERT: A 348 PHE cc_start: 0.8201 (t80) cc_final: 0.7953 (t80) REVERT: A 653 TRP cc_start: 0.5997 (t-100) cc_final: 0.5716 (t-100) REVERT: A 732 GLU cc_start: 0.5837 (mt-10) cc_final: 0.5421 (tp30) REVERT: B 263 ARG cc_start: 0.7994 (tpt170) cc_final: 0.7588 (ptt-90) REVERT: B 341 GLN cc_start: 0.8519 (mt0) cc_final: 0.8219 (tt0) REVERT: B 547 TYR cc_start: 0.8231 (t80) cc_final: 0.7825 (t80) outliers start: 33 outliers final: 22 residues processed: 139 average time/residue: 0.0907 time to fit residues: 17.7050 Evaluate side-chains 125 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain B residue 546 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 HIS ** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.143897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.108905 restraints weight = 50784.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.106859 restraints weight = 38820.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.107727 restraints weight = 29222.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.108682 restraints weight = 23992.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.108960 restraints weight = 20239.899| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11860 Z= 0.170 Angle : 0.632 8.139 16411 Z= 0.337 Chirality : 0.043 0.301 1823 Planarity : 0.006 0.089 1885 Dihedral : 18.567 127.321 2566 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.14 % Allowed : 17.90 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.24), residues: 1221 helix: 0.83 (0.23), residues: 484 sheet: -0.74 (0.38), residues: 183 loop : -0.04 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 199 TYR 0.031 0.002 TYR B 481 PHE 0.022 0.002 PHE B 292 TRP 0.010 0.001 TRP B 425 HIS 0.004 0.001 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (11860) covalent geometry : angle 0.63199 / 0.34 (16411) hydrogen bonds : bond 0.04875 / 3.20 ( 499) hydrogen bonds : angle 5.43818 / 4.03 ( 1368) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7445 (mm-30) REVERT: A 107 MET cc_start: 0.7436 (mtp) cc_final: 0.6861 (mtt) REVERT: A 116 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8138 (mm) REVERT: A 124 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.5582 (ppt170) REVERT: A 324 ASN cc_start: 0.8084 (t0) cc_final: 0.7318 (m-40) REVERT: A 342 MET cc_start: 0.6166 (mpp) cc_final: 0.4857 (mpp) REVERT: A 379 MET cc_start: 0.7537 (tpt) cc_final: 0.7302 (tpt) REVERT: A 496 MET cc_start: 0.8053 (mmm) cc_final: 0.7319 (tpp) REVERT: A 653 TRP cc_start: 0.4957 (t-100) cc_final: 0.4741 (t-100) REVERT: A 886 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5541 (mm) REVERT: B 341 GLN cc_start: 0.8418 (mt0) cc_final: 0.8109 (tt0) REVERT: B 547 TYR cc_start: 0.8256 (t80) cc_final: 0.7539 (t80) outliers start: 33 outliers final: 22 residues processed: 134 average time/residue: 0.1076 time to fit residues: 20.1500 Evaluate side-chains 125 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain B residue 546 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 123 optimal weight: 40.0000 chunk 120 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 HIS ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.142844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.107680 restraints weight = 50281.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.105830 restraints weight = 38118.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.107094 restraints weight = 28546.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.107858 restraints weight = 22962.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.108199 restraints weight = 19683.257| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11860 Z= 0.158 Angle : 0.612 7.120 16411 Z= 0.323 Chirality : 0.042 0.292 1823 Planarity : 0.005 0.075 1885 Dihedral : 18.487 126.457 2566 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.33 % Allowed : 18.00 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1221 helix: 0.88 (0.23), residues: 484 sheet: -0.66 (0.41), residues: 162 loop : -0.09 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 523 TYR 0.046 0.002 TYR B 481 PHE 0.021 0.002 PHE B 591 TRP 0.009 0.001 TRP B 553 HIS 0.004 0.001 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (11860) covalent geometry : angle 0.61190 / 0.32 (16411) hydrogen bonds : bond 0.04616 / 3.04 ( 499) hydrogen bonds : angle 5.38184 / 3.99 ( 1368) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7447 (mm-30) REVERT: A 107 MET cc_start: 0.7510 (mtp) cc_final: 0.6878 (mtt) REVERT: A 116 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8130 (mm) REVERT: A 124 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6067 (ppt170) REVERT: A 324 ASN cc_start: 0.8189 (t0) cc_final: 0.7466 (m-40) REVERT: A 342 MET cc_start: 0.5979 (mpp) cc_final: 0.5710 (mpp) REVERT: A 379 MET cc_start: 0.7520 (tpt) cc_final: 0.7172 (tpt) REVERT: A 496 MET cc_start: 0.8123 (mmm) cc_final: 0.7417 (tpp) REVERT: A 886 LEU cc_start: 0.5759 (OUTLIER) cc_final: 0.5366 (mm) REVERT: B 341 GLN cc_start: 0.8443 (mt0) cc_final: 0.8181 (tt0) REVERT: B 534 MET cc_start: 0.7581 (tpp) cc_final: 0.7119 (tpp) REVERT: B 547 TYR cc_start: 0.8290 (t80) cc_final: 0.7728 (t80) outliers start: 35 outliers final: 24 residues processed: 134 average time/residue: 0.0980 time to fit residues: 18.6930 Evaluate side-chains 128 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain B residue 546 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 4 optimal weight: 0.1980 chunk 123 optimal weight: 40.0000 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.146542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.110756 restraints weight = 51422.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.108929 restraints weight = 38600.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.109797 restraints weight = 27421.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.109654 restraints weight = 22859.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.109968 restraints weight = 19296.502| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11860 Z= 0.146 Angle : 0.635 9.652 16411 Z= 0.331 Chirality : 0.042 0.285 1823 Planarity : 0.005 0.069 1885 Dihedral : 18.464 125.026 2566 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.33 % Allowed : 18.95 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1221 helix: 0.72 (0.23), residues: 490 sheet: -0.69 (0.41), residues: 162 loop : -0.11 (0.28), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 263 TYR 0.049 0.002 TYR B 481 PHE 0.021 0.002 PHE B 292 TRP 0.025 0.002 TRP A 653 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (11860) covalent geometry : angle 0.63458 / 0.33 (16411) hydrogen bonds : bond 0.04539 / 2.97 ( 499) hydrogen bonds : angle 5.33203 / 3.95 ( 1368) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7463 (mm-30) REVERT: A 107 MET cc_start: 0.7505 (mtp) cc_final: 0.6880 (mtt) REVERT: A 116 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8145 (mm) REVERT: A 124 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.6136 (ppt170) REVERT: A 324 ASN cc_start: 0.8099 (t0) cc_final: 0.7688 (m-40) REVERT: A 342 MET cc_start: 0.6043 (mpp) cc_final: 0.5802 (mpp) REVERT: A 379 MET cc_start: 0.7561 (tpt) cc_final: 0.6940 (tpt) REVERT: A 496 MET cc_start: 0.8145 (mmm) cc_final: 0.7567 (tpp) REVERT: A 709 CYS cc_start: -0.4901 (p) cc_final: -0.5352 (p) REVERT: A 886 LEU cc_start: 0.4556 (OUTLIER) cc_final: 0.3994 (mm) REVERT: B 341 GLN cc_start: 0.8280 (mt0) cc_final: 0.7984 (tt0) REVERT: B 534 MET cc_start: 0.7560 (tpp) cc_final: 0.6984 (tpp) REVERT: B 547 TYR cc_start: 0.8232 (t80) cc_final: 0.7663 (t80) REVERT: B 570 MET cc_start: 0.8573 (mtp) cc_final: 0.8150 (mmm) outliers start: 35 outliers final: 27 residues processed: 134 average time/residue: 0.0941 time to fit residues: 18.6500 Evaluate side-chains 128 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain B residue 546 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 32 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.145745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.109057 restraints weight = 51983.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.106254 restraints weight = 42570.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.106618 restraints weight = 32116.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.106716 restraints weight = 23952.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.107225 restraints weight = 21989.865| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11860 Z= 0.157 Angle : 0.630 9.536 16411 Z= 0.331 Chirality : 0.042 0.280 1823 Planarity : 0.005 0.062 1885 Dihedral : 18.450 124.339 2566 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.33 % Allowed : 19.43 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.25), residues: 1221 helix: 0.75 (0.23), residues: 485 sheet: -0.97 (0.41), residues: 160 loop : -0.07 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 199 TYR 0.020 0.002 TYR A 547 PHE 0.023 0.002 PHE B 292 TRP 0.024 0.002 TRP A 653 HIS 0.004 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (11860) covalent geometry : angle 0.63049 / 0.33 (16411) hydrogen bonds : bond 0.04533 / 3.00 ( 499) hydrogen bonds : angle 5.29005 / 3.92 ( 1368) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7512 (mm-30) REVERT: A 107 MET cc_start: 0.7529 (mtp) cc_final: 0.6948 (mtt) REVERT: A 116 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8110 (mm) REVERT: A 124 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6122 (ppt170) REVERT: A 324 ASN cc_start: 0.8079 (t0) cc_final: 0.7693 (m-40) REVERT: A 342 MET cc_start: 0.6226 (mpp) cc_final: 0.5945 (mpp) REVERT: A 496 MET cc_start: 0.8297 (mmm) cc_final: 0.7761 (tpp) REVERT: A 709 CYS cc_start: -0.5351 (p) cc_final: -0.5778 (p) REVERT: A 886 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5409 (mm) REVERT: B 534 MET cc_start: 0.7608 (tpp) cc_final: 0.7029 (tpp) REVERT: B 547 TYR cc_start: 0.8183 (t80) cc_final: 0.7926 (t80) outliers start: 35 outliers final: 28 residues processed: 129 average time/residue: 0.0926 time to fit residues: 17.7490 Evaluate side-chains 126 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 551 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 7.9990 chunk 122 optimal weight: 40.0000 chunk 58 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.136803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.102056 restraints weight = 50099.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.100560 restraints weight = 38389.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.101478 restraints weight = 28215.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.102556 restraints weight = 23131.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.102830 restraints weight = 19380.305| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11860 Z= 0.246 Angle : 0.746 9.993 16411 Z= 0.399 Chirality : 0.046 0.289 1823 Planarity : 0.006 0.062 1885 Dihedral : 18.693 125.402 2566 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 24.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.90 % Allowed : 18.86 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.24), residues: 1221 helix: 0.21 (0.23), residues: 483 sheet: -1.06 (0.37), residues: 191 loop : -0.34 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 408 TYR 0.028 0.003 TYR A 547 PHE 0.030 0.003 PHE B 292 TRP 0.032 0.003 TRP A 653 HIS 0.008 0.002 HIS A 558 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.25 (11860) covalent geometry : angle 0.74597 / 0.40 (16411) hydrogen bonds : bond 0.05861 / 3.87 ( 499) hydrogen bonds : angle 5.76489 / 4.27 ( 1368) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8000 (mm) REVERT: A 124 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.5635 (ppt170) REVERT: A 324 ASN cc_start: 0.8414 (t0) cc_final: 0.8036 (m-40) REVERT: A 342 MET cc_start: 0.6618 (mpp) cc_final: 0.6360 (mpp) REVERT: A 496 MET cc_start: 0.8320 (mmm) cc_final: 0.7846 (tpp) REVERT: A 886 LEU cc_start: 0.4747 (OUTLIER) cc_final: 0.4233 (mm) outliers start: 41 outliers final: 31 residues processed: 128 average time/residue: 0.0858 time to fit residues: 16.2555 Evaluate side-chains 126 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 551 PHE Chi-restraints excluded: chain B residue 578 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 61 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 126 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.140694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.106750 restraints weight = 51124.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.104122 restraints weight = 40441.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.104899 restraints weight = 29143.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.105805 restraints weight = 23666.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.106636 restraints weight = 20667.429| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11860 Z= 0.152 Angle : 0.677 15.214 16411 Z= 0.352 Chirality : 0.043 0.274 1823 Planarity : 0.006 0.058 1885 Dihedral : 18.633 122.071 2566 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.86 % Allowed : 19.81 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1221 helix: 0.55 (0.23), residues: 484 sheet: -1.17 (0.38), residues: 180 loop : -0.27 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 199 TYR 0.033 0.002 TYR B 481 PHE 0.022 0.002 PHE B 292 TRP 0.022 0.002 TRP A 653 HIS 0.004 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (11860) covalent geometry : angle 0.67700 / 0.35 (16411) hydrogen bonds : bond 0.04658 / 3.05 ( 499) hydrogen bonds : angle 5.40642 / 4.00 ( 1368) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.7525 (mtp) cc_final: 0.6921 (mtt) REVERT: A 116 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8007 (mm) REVERT: A 124 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.5836 (ppt170) REVERT: A 324 ASN cc_start: 0.8236 (t0) cc_final: 0.7861 (m-40) REVERT: A 342 MET cc_start: 0.6546 (mpp) cc_final: 0.6161 (mpp) REVERT: A 496 MET cc_start: 0.8259 (mmm) cc_final: 0.7904 (tpt) REVERT: A 570 MET cc_start: 0.6227 (ttt) cc_final: 0.6024 (ttt) REVERT: A 709 CYS cc_start: -0.4478 (p) cc_final: -0.4824 (p) REVERT: A 717 LEU cc_start: 0.7156 (mt) cc_final: 0.6799 (pp) REVERT: A 886 LEU cc_start: 0.5156 (OUTLIER) cc_final: 0.4697 (mm) REVERT: B 534 MET cc_start: 0.7636 (tpp) cc_final: 0.6965 (tpt) outliers start: 30 outliers final: 23 residues processed: 121 average time/residue: 0.0822 time to fit residues: 14.9848 Evaluate side-chains 120 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 653 TRP Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 551 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 11 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 68 optimal weight: 30.0000 chunk 91 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.139922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.096900 restraints weight = 51793.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.098072 restraints weight = 36054.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.099292 restraints weight = 29267.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.099744 restraints weight = 25241.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.100291 restraints weight = 23095.579| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11860 Z= 0.196 Angle : 0.695 13.965 16411 Z= 0.367 Chirality : 0.044 0.266 1823 Planarity : 0.006 0.049 1885 Dihedral : 18.594 120.612 2566 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.57 % Allowed : 20.95 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.24), residues: 1221 helix: 0.43 (0.23), residues: 484 sheet: -1.24 (0.39), residues: 180 loop : -0.42 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 408 TYR 0.038 0.002 TYR B 481 PHE 0.027 0.002 PHE B 292 TRP 0.019 0.002 TRP A 653 HIS 0.005 0.001 HIS A 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (11860) covalent geometry : angle 0.69478 / 0.37 (16411) hydrogen bonds : bond 0.05136 / 3.36 ( 499) hydrogen bonds : angle 5.53331 / 4.10 ( 1368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2229.33 seconds wall clock time: 39 minutes 0.50 seconds (2340.50 seconds total)