Starting phenix.real_space_refine on Fri Oct 23 11:17:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30jz_57835/10_2026/30jz_57835.cif Found real_map, /net/cci-nas-00/data/ceres_data/30jz_57835/10_2026/30jz_57835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/30jz_57835/10_2026/30jz_57835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30jz_57835/10_2026/30jz_57835.map" model { file = "/net/cci-nas-00/data/ceres_data/30jz_57835/10_2026/30jz_57835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30jz_57835/10_2026/30jz_57835.cif" } resolution = 3.6 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= 0.001 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 6166 2.51 5 N 1599 2.21 5 O 1824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9648 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 8210 Classifications: {'peptide': 1013} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 968} Chain: "B" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1405 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.95, per 1000 atoms: 0.20 Number of scatterers: 9648 At special positions: 0 Unit cell: (113.424, 91.74, 106.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 3 15.00 Mg 1 11.99 O 1824 8.00 N 1599 7.00 C 6166 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: 0.88 Conformation dependent library (CDL) restraints added in 350.4 milliseconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 1 sheets defined 74.6% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.695A pdb=" N LEU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 49 through 68 Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 94 through 101 Processing helix chain 'A' and resid 103 through 122 removed outlier: 3.807A pdb=" N GLN A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 138 removed outlier: 4.044A pdb=" N GLU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.578A pdb=" N ASN A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 167 through 189 removed outlier: 4.069A pdb=" N HIS A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 193 through 211 Processing helix chain 'A' and resid 221 through 238 Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 255 through 276 Processing helix chain 'A' and resid 285 through 313 removed outlier: 3.863A pdb=" N LYS A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLY A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 306 " --> pdb=" O GLN A 302 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 307 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 333 Processing helix chain 'A' and resid 335 through 353 Proline residue: A 344 - end of helix removed outlier: 4.653A pdb=" N GLN A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLY A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 361 through 371 Processing helix chain 'A' and resid 371 through 379 Processing helix chain 'A' and resid 388 through 404 Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.701A pdb=" N GLU A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 439 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 461 through 467 Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 490 through 508 removed outlier: 3.859A pdb=" N LEU A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 528 Processing helix chain 'A' and resid 529 through 535 removed outlier: 4.895A pdb=" N GLU A 533 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 535 " --> pdb=" O LYS A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 554 removed outlier: 3.902A pdb=" N VAL A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU A 552 " --> pdb=" O HIS A 548 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 554 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 569 through 595 removed outlier: 4.064A pdb=" N THR A 574 " --> pdb=" O SER A 570 " (cutoff:3.500A) Proline residue: A 575 - end of helix removed outlier: 3.752A pdb=" N THR A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY A 595 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 622 Processing helix chain 'A' and resid 625 through 647 removed outlier: 3.824A pdb=" N GLN A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 632 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE A 635 " --> pdb=" O GLN A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 651 through 663 removed outlier: 3.960A pdb=" N SER A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 673 removed outlier: 3.508A pdb=" N TRP A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A 673 " --> pdb=" O PRO A 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 668 through 673' Processing helix chain 'A' and resid 673 through 684 removed outlier: 4.363A pdb=" N LEU A 677 " --> pdb=" O GLN A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 704 Proline residue: A 695 - end of helix removed outlier: 3.872A pdb=" N ASP A 704 " --> pdb=" O TYR A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 removed outlier: 3.938A pdb=" N ASP A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 728 Processing helix chain 'A' and resid 731 through 749 removed outlier: 3.509A pdb=" N CYS A 749 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 771 removed outlier: 4.202A pdb=" N LEU A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 771 " --> pdb=" O GLU A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 793 removed outlier: 3.706A pdb=" N ALA A 786 " --> pdb=" O CYS A 782 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 803 removed outlier: 3.555A pdb=" N ASN A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 824 removed outlier: 4.177A pdb=" N HIS A 816 " --> pdb=" O PRO A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 828 removed outlier: 3.593A pdb=" N PHE A 828 " --> pdb=" O VAL A 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 825 through 828' Processing helix chain 'A' and resid 830 through 845 Processing helix chain 'A' and resid 851 through 887 removed outlier: 3.607A pdb=" N ASN A 855 " --> pdb=" O PRO A 851 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N SER A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN A 860 " --> pdb=" O GLN A 856 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 862 " --> pdb=" O SER A 858 " (cutoff:3.500A) Proline residue: A 863 - end of helix removed outlier: 3.661A pdb=" N GLY A 871 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 874 " --> pdb=" O ASN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 923 removed outlier: 3.717A pdb=" N GLU A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 973 Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 985 through 1013 removed outlier: 3.606A pdb=" N LYS A1013 " --> pdb=" O LYS A1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 32 Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.652A pdb=" N ILE B 81 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 100 removed outlier: 4.195A pdb=" N TYR B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 158 through 170 Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 54 removed outlier: 6.082A pdb=" N VAL B 9 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASN B 62 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE B 11 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TRP B 64 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU B 13 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N THR B 66 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU B 15 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N CYS B 85 " --> pdb=" O GLN B 10 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LYS B 12 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE B 87 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 14 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N MET B 89 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 16 " --> pdb=" O MET B 89 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ASP B 91 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 145 " --> pdb=" O ILE B 117 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3170 1.34 - 1.46: 2115 1.46 - 1.58: 4481 1.58 - 1.70: 5 1.70 - 1.82: 85 Bond restraints: 9856 Sorted by residual: bond pdb=" CA GLU A 846 " pdb=" CB GLU A 846 " ideal model delta sigma weight residual 1.528 1.562 -0.035 1.39e-02 5.18e+03 6.21e+00 bond pdb=" C HIS B 48 " pdb=" N PRO B 49 " ideal model delta sigma weight residual 1.334 1.318 0.016 1.11e-02 8.12e+03 2.07e+00 bond pdb=" CB GLU A 943 " pdb=" CG GLU A 943 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.00e+00 bond pdb=" CA THR B 42 " pdb=" C THR B 42 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.24e-02 6.50e+03 1.63e+00 bond pdb=" CG1 ILE A 787 " pdb=" CD1 ILE A 787 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.62e+00 ... (remaining 9851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 13072 1.98 - 3.96: 242 3.96 - 5.94: 50 5.94 - 7.92: 6 7.92 - 9.90: 5 Bond angle restraints: 13375 Sorted by residual: angle pdb=" C ASP A 957 " pdb=" N GLU A 958 " pdb=" CA GLU A 958 " ideal model delta sigma weight residual 121.54 130.49 -8.95 1.91e+00 2.74e-01 2.20e+01 angle pdb=" N ASP B 77 " pdb=" CA ASP B 77 " pdb=" C ASP B 77 " ideal model delta sigma weight residual 114.62 110.45 4.17 1.14e+00 7.69e-01 1.34e+01 angle pdb=" CA GLN A 41 " pdb=" CB GLN A 41 " pdb=" CG GLN A 41 " ideal model delta sigma weight residual 114.10 120.91 -6.81 2.00e+00 2.50e-01 1.16e+01 angle pdb=" N GLY A 686 " pdb=" CA GLY A 686 " pdb=" C GLY A 686 " ideal model delta sigma weight residual 115.34 109.66 5.68 1.67e+00 3.59e-01 1.16e+01 angle pdb=" CB MET A 857 " pdb=" CG MET A 857 " pdb=" SD MET A 857 " ideal model delta sigma weight residual 112.70 122.60 -9.90 3.00e+00 1.11e-01 1.09e+01 ... (remaining 13370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.55: 5685 29.55 - 59.09: 238 59.09 - 88.64: 42 88.64 - 118.19: 1 118.19 - 147.74: 3 Dihedral angle restraints: 5969 sinusoidal: 2469 harmonic: 3500 Sorted by residual: dihedral pdb=" C8 GTP B 201 " pdb=" C1' GTP B 201 " pdb=" N9 GTP B 201 " pdb=" O4' GTP B 201 " ideal model delta sinusoidal sigma weight residual 104.59 -43.14 147.74 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O3B GTP B 201 " pdb=" O3A GTP B 201 " pdb=" PB GTP B 201 " pdb=" PA GTP B 201 " ideal model delta sinusoidal sigma weight residual 291.08 158.11 132.97 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O5' GTP B 201 " pdb=" O3A GTP B 201 " pdb=" PA GTP B 201 " pdb=" PB GTP B 201 " ideal model delta sinusoidal sigma weight residual 274.12 147.08 127.04 1 2.00e+01 2.50e-03 3.85e+01 ... (remaining 5966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 808 0.030 - 0.060: 445 0.060 - 0.090: 169 0.090 - 0.120: 64 0.120 - 0.150: 12 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CA HIS A 460 " pdb=" N HIS A 460 " pdb=" C HIS A 460 " pdb=" CB HIS A 460 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CG LEU A 797 " pdb=" CB LEU A 797 " pdb=" CD1 LEU A 797 " pdb=" CD2 LEU A 797 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE A 317 " pdb=" N ILE A 317 " pdb=" C ILE A 317 " pdb=" CB ILE A 317 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 1495 not shown) Planarity restraints: 1721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 958 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C GLU A 958 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU A 958 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR A 959 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 191 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A 192 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 171 " -0.028 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO B 172 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 172 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 172 " -0.024 5.00e-02 4.00e+02 ... (remaining 1718 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 6 2.48 - 3.08: 7166 3.08 - 3.69: 14873 3.69 - 4.29: 20658 4.29 - 4.90: 33635 Nonbonded interactions: 76338 Sorted by model distance: nonbonded pdb=" OG1 THR B 42 " pdb="MG MG B 202 " model vdw 1.872 2.170 nonbonded pdb=" O1G GTP B 201 " pdb="MG MG B 202 " model vdw 1.930 2.170 nonbonded pdb=" O2B GTP B 201 " pdb="MG MG B 202 " model vdw 1.935 2.170 nonbonded pdb=" OG1 THR B 24 " pdb="MG MG B 202 " model vdw 2.205 2.170 nonbonded pdb=" O2' GTP B 201 " pdb=" O3' GTP B 201 " model vdw 2.474 2.432 ... (remaining 76333 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: 0.010 Normalize map: mean=0, sd=1: 0.180 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.190 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.005 0.050 9856 Z= 0.212 Angle : 0.717 9.903 13375 Z= 0.389 Chirality : 0.044 0.150 1498 Planarity : 0.004 0.044 1721 Dihedral : 16.820 147.737 3697 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.75 % Allowed : 15.25 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: 1.40 (0.25), residues: 1182 helix: 1.49 (0.19), residues: 793 sheet: -0.95 (0.70), residues: 50 loop : 0.06 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 502 TYR 0.018 0.002 TYR A 360 PHE 0.014 0.001 PHE A 798 TRP 0.012 0.002 TRP A 145 HIS 0.008 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 ( 9856) covalent geometry : angle 0.71664 / 0.39 (13375) hydrogen bonds : bond 0.14282 / 9.72 ( 588) hydrogen bonds : angle 5.48547 / 4.01 ( 1722) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7784 (m-30) cc_final: 0.7298 (t0) REVERT: A 100 MET cc_start: 0.8296 (mmm) cc_final: 0.7983 (mtt) REVERT: A 305 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8616 (mt) REVERT: A 412 MET cc_start: 0.7992 (mmm) cc_final: 0.7259 (mmm) REVERT: A 472 MET cc_start: 0.8434 (tpp) cc_final: 0.8064 (tpp) REVERT: A 487 LYS cc_start: 0.9272 (mttt) cc_final: 0.8881 (mtmm) REVERT: A 693 MET cc_start: 0.8618 (mtm) cc_final: 0.8233 (ttm) REVERT: A 735 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8527 (mt-10) REVERT: A 970 GLN cc_start: 0.7262 (tt0) cc_final: 0.6431 (tm-30) REVERT: A 977 TYR cc_start: 0.8167 (t80) cc_final: 0.7964 (t80) REVERT: A 1010 MET cc_start: 0.7562 (ttm) cc_final: 0.5603 (tmm) REVERT: B 36 GLU cc_start: 0.8761 (tp30) cc_final: 0.8433 (tp30) REVERT: B 122 ASN cc_start: 0.9485 (t0) cc_final: 0.9107 (t0) REVERT: B 145 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8008 (tp-100) REVERT: B 149 ILE cc_start: 0.9333 (pp) cc_final: 0.8560 (pt) REVERT: B 156 ASN cc_start: 0.8857 (m-40) cc_final: 0.7890 (m110) REVERT: B 171 ASP cc_start: 0.8972 (m-30) cc_final: 0.8506 (m-30) REVERT: B 175 GLU cc_start: 0.8390 (tt0) cc_final: 0.7782 (mm-30) outliers start: 8 outliers final: 5 residues processed: 109 average time/residue: 0.0824 time to fit residues: 13.4849 Evaluate side-chains 93 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 93 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.0870 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN ** A 158 ASN ** 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 = 0.3422 r_free = 0.3422 target = 0.097725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.078145 restraints weight = 20871.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.081150 restraints weight = 10356.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.083203 restraints weight = 6651.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.084561 restraints weight = 4932.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085394 restraints weight = 4026.698| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9856 Z= 0.130 Angle : 0.556 7.888 13375 Z= 0.284 Chirality : 0.041 0.150 1498 Planarity : 0.004 0.039 1721 Dihedral : 8.763 147.371 1300 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.26 % Allowed : 16.10 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: 1.97 (0.25), residues: 1182 helix: 1.94 (0.19), residues: 791 sheet: -0.66 (0.72), residues: 50 loop : 0.23 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 76 TYR 0.010 0.001 TYR A 471 PHE 0.012 0.001 PHE A 687 TRP 0.007 0.001 TRP A 976 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9856) covalent geometry : angle 0.55638 / 0.28 (13375) hydrogen bonds : bond 0.04043 / 2.78 ( 588) hydrogen bonds : angle 4.27123 / 3.14 ( 1722) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7815 (m-30) cc_final: 0.7389 (t0) REVERT: A 100 MET cc_start: 0.8213 (mmm) cc_final: 0.7919 (mtt) REVERT: A 301 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 487 LYS cc_start: 0.9280 (mttt) cc_final: 0.8882 (mtmm) REVERT: A 543 MET cc_start: 0.8332 (mmm) cc_final: 0.8018 (mmm) REVERT: A 693 MET cc_start: 0.8646 (mtm) cc_final: 0.8389 (ttm) REVERT: A 735 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8157 (mt-10) REVERT: A 970 GLN cc_start: 0.7205 (tt0) cc_final: 0.6372 (tm-30) REVERT: A 977 TYR cc_start: 0.8216 (t80) cc_final: 0.7964 (t80) REVERT: A 1010 MET cc_start: 0.7697 (ttm) cc_final: 0.5892 (tmm) REVERT: B 36 GLU cc_start: 0.8649 (tp30) cc_final: 0.8443 (tp30) REVERT: B 89 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7570 (ttp) REVERT: B 122 ASN cc_start: 0.9365 (t0) cc_final: 0.9033 (t0) REVERT: B 145 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8056 (tp-100) REVERT: B 149 ILE cc_start: 0.9420 (pp) cc_final: 0.8562 (pt) REVERT: B 156 ASN cc_start: 0.8930 (m-40) cc_final: 0.8054 (m110) REVERT: B 171 ASP cc_start: 0.8954 (m-30) cc_final: 0.8543 (m-30) REVERT: B 175 GLU cc_start: 0.8234 (tt0) cc_final: 0.7812 (mm-30) outliers start: 24 outliers final: 16 residues processed: 119 average time/residue: 0.0787 time to fit residues: 14.2514 Evaluate side-chains 104 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 925 GLU Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 166 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [107, 58, 116, 110, 18, 114, 68, 62, 69, 108, 10] chunk 107 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 HIS A 922 GLN B 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.098776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.079140 restraints weight = 21138.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.082237 restraints weight = 10458.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.084294 restraints weight = 6705.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.085661 restraints weight = 4995.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086630 restraints weight = 4081.879| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9856 Z= 0.112 Angle : 0.518 7.267 13375 Z= 0.261 Chirality : 0.040 0.153 1498 Planarity : 0.004 0.040 1721 Dihedral : 8.361 146.585 1296 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.17 % Allowed : 16.76 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.25), residues: 1182 helix: 2.06 (0.19), residues: 794 sheet: -0.27 (0.78), residues: 47 loop : 0.24 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.011 0.001 TYR A 360 PHE 0.008 0.001 PHE A 538 TRP 0.012 0.001 TRP A 68 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9856) covalent geometry : angle 0.51818 / 0.26 (13375) hydrogen bonds : bond 0.03576 / 2.47 ( 588) hydrogen bonds : angle 4.04764 / 2.98 ( 1722) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7781 (m-30) cc_final: 0.7412 (t0) REVERT: A 100 MET cc_start: 0.8167 (mmm) cc_final: 0.7823 (mtt) REVERT: A 412 MET cc_start: 0.7948 (tpp) cc_final: 0.7239 (mmm) REVERT: A 472 MET cc_start: 0.8539 (tpp) cc_final: 0.8277 (tpt) REVERT: A 482 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8027 (t80) REVERT: A 487 LYS cc_start: 0.9286 (mttt) cc_final: 0.8891 (mtmm) REVERT: A 543 MET cc_start: 0.8516 (mmm) cc_final: 0.7963 (mmm) REVERT: A 569 TYR cc_start: 0.7873 (m-80) cc_final: 0.7540 (m-10) REVERT: A 735 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8111 (mt-10) REVERT: A 958 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7045 (pm20) REVERT: A 970 GLN cc_start: 0.7176 (tt0) cc_final: 0.6396 (tm-30) REVERT: A 977 TYR cc_start: 0.8240 (t80) cc_final: 0.8035 (t80) REVERT: A 1010 MET cc_start: 0.7612 (ttm) cc_final: 0.5869 (tmm) REVERT: B 18 ASP cc_start: 0.8090 (t70) cc_final: 0.7438 (t0) REVERT: B 36 GLU cc_start: 0.8574 (tp30) cc_final: 0.8354 (tp30) REVERT: B 122 ASN cc_start: 0.9299 (t0) cc_final: 0.8984 (t0) REVERT: B 149 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.8592 (pt) REVERT: B 156 ASN cc_start: 0.8952 (m-40) cc_final: 0.8046 (m110) REVERT: B 171 ASP cc_start: 0.8942 (m-30) cc_final: 0.8533 (m-30) outliers start: 23 outliers final: 15 residues processed: 116 average time/residue: 0.0732 time to fit residues: 12.8310 Evaluate side-chains 106 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 958 GLU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [73, 58, 48, 106, 45, 112, 84, 97, 98, 79, 49] chunk 73 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076965 restraints weight = 21248.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.080023 restraints weight = 10469.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082065 restraints weight = 6692.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.083393 restraints weight = 4965.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.084324 restraints weight = 4061.466| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9856 Z= 0.160 Angle : 0.554 7.015 13375 Z= 0.281 Chirality : 0.041 0.151 1498 Planarity : 0.004 0.040 1721 Dihedral : 8.379 148.564 1293 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.11 % Allowed : 17.23 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.25), residues: 1182 helix: 2.12 (0.19), residues: 788 sheet: -0.17 (0.79), residues: 45 loop : 0.26 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 53 TYR 0.016 0.001 TYR A 360 PHE 0.010 0.001 PHE A 798 TRP 0.009 0.001 TRP A 976 HIS 0.012 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 9856) covalent geometry : angle 0.55437 / 0.28 (13375) hydrogen bonds : bond 0.03819 / 2.64 ( 588) hydrogen bonds : angle 4.06397 / 3.00 ( 1722) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7791 (m-30) cc_final: 0.7469 (t0) REVERT: A 301 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7716 (tm-30) REVERT: A 412 MET cc_start: 0.7881 (tpp) cc_final: 0.7150 (mmm) REVERT: A 456 MET cc_start: 0.7084 (tpp) cc_final: 0.6726 (ttm) REVERT: A 472 MET cc_start: 0.8559 (tpp) cc_final: 0.8277 (tpt) REVERT: A 482 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.7980 (t80) REVERT: A 487 LYS cc_start: 0.9303 (mttt) cc_final: 0.8911 (mtmm) REVERT: A 543 MET cc_start: 0.8586 (mmm) cc_final: 0.7953 (mmm) REVERT: A 569 TYR cc_start: 0.7482 (m-80) cc_final: 0.7221 (m-10) REVERT: A 735 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8171 (mt-10) REVERT: A 958 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7032 (pm20) REVERT: A 970 GLN cc_start: 0.7252 (tt0) cc_final: 0.6417 (tm-30) REVERT: A 977 TYR cc_start: 0.8207 (t80) cc_final: 0.7981 (t80) REVERT: A 1010 MET cc_start: 0.7723 (ttm) cc_final: 0.5905 (tmm) REVERT: B 18 ASP cc_start: 0.8124 (t70) cc_final: 0.7498 (t0) REVERT: B 30 HIS cc_start: 0.8743 (OUTLIER) cc_final: 0.8337 (m-70) REVERT: B 36 GLU cc_start: 0.8612 (tp30) cc_final: 0.8407 (tp30) REVERT: B 122 ASN cc_start: 0.9303 (t0) cc_final: 0.8998 (t0) REVERT: B 149 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.8570 (pt) REVERT: B 156 ASN cc_start: 0.8984 (m-40) cc_final: 0.8729 (m-40) REVERT: B 171 ASP cc_start: 0.9016 (m-30) cc_final: 0.8561 (m-30) outliers start: 33 outliers final: 22 residues processed: 120 average time/residue: 0.0778 time to fit residues: 14.1901 Evaluate side-chains 112 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 958 GLU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [45, 36, 93, 71, 48, 67, 37, 49, 102, 81, 108] chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 93 optimal weight: 0.0060 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 81 optimal weight: 0.0570 chunk 108 optimal weight: 1.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 HIS A 784 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.080334 restraints weight = 20817.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.083447 restraints weight = 10085.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.085515 restraints weight = 6356.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.086922 restraints weight = 4672.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087891 restraints weight = 3765.973| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9856 Z= 0.100 Angle : 0.503 7.628 13375 Z= 0.251 Chirality : 0.039 0.146 1498 Planarity : 0.004 0.041 1721 Dihedral : 8.324 145.950 1293 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.26 % Allowed : 17.61 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.25), residues: 1182 helix: 2.20 (0.19), residues: 792 sheet: -0.24 (0.75), residues: 50 loop : 0.38 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 53 TYR 0.008 0.001 TYR A 360 PHE 0.008 0.001 PHE A 687 TRP 0.012 0.001 TRP A 68 HIS 0.006 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 9856) covalent geometry : angle 0.50286 / 0.25 (13375) hydrogen bonds : bond 0.03175 / 2.20 ( 588) hydrogen bonds : angle 3.88604 / 2.85 ( 1722) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7677 (m-30) cc_final: 0.7320 (t0) REVERT: A 301 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7718 (tm-30) REVERT: A 412 MET cc_start: 0.7807 (tpp) cc_final: 0.7027 (mmm) REVERT: A 472 MET cc_start: 0.8535 (tpp) cc_final: 0.8251 (tpt) REVERT: A 482 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8032 (t80) REVERT: A 487 LYS cc_start: 0.9295 (mttt) cc_final: 0.8893 (mtmm) REVERT: A 543 MET cc_start: 0.8457 (mmm) cc_final: 0.8118 (mmm) REVERT: A 735 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8082 (mt-10) REVERT: A 781 MET cc_start: 0.9149 (mmm) cc_final: 0.8916 (mmm) REVERT: A 958 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7084 (pm20) REVERT: A 968 LYS cc_start: 0.8425 (pttt) cc_final: 0.7301 (mmtm) REVERT: A 970 GLN cc_start: 0.7168 (tt0) cc_final: 0.6425 (tm-30) REVERT: A 977 TYR cc_start: 0.8158 (t80) cc_final: 0.7940 (t80) REVERT: A 1010 MET cc_start: 0.7638 (ttm) cc_final: 0.5890 (tmm) REVERT: B 18 ASP cc_start: 0.8132 (t70) cc_final: 0.7449 (t0) REVERT: B 30 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8254 (m-70) REVERT: B 36 GLU cc_start: 0.8634 (tp30) cc_final: 0.8380 (tp30) REVERT: B 122 ASN cc_start: 0.9247 (t0) cc_final: 0.8992 (t0) REVERT: B 149 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.8532 (pt) REVERT: B 156 ASN cc_start: 0.8957 (m-40) cc_final: 0.8704 (m-40) REVERT: B 171 ASP cc_start: 0.8927 (m-30) cc_final: 0.8457 (m-30) outliers start: 24 outliers final: 17 residues processed: 118 average time/residue: 0.0799 time to fit residues: 14.1073 Evaluate side-chains 110 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 958 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [38, 69, 115, 59, 97, 90, 114, 110, 20, 52, 58] chunk 38 optimal weight: 0.0870 chunk 69 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** 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 = 0.3429 r_free = 0.3429 target = 0.098390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.079267 restraints weight = 20819.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.082344 restraints weight = 10083.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.084416 restraints weight = 6383.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085816 restraints weight = 4692.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.086768 restraints weight = 3795.556| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9856 Z= 0.113 Angle : 0.510 6.883 13375 Z= 0.255 Chirality : 0.040 0.148 1498 Planarity : 0.004 0.040 1721 Dihedral : 8.286 146.589 1293 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.64 % Allowed : 17.98 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.25), residues: 1182 helix: 2.24 (0.19), residues: 790 sheet: -0.52 (0.74), residues: 53 loop : 0.43 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 110 TYR 0.011 0.001 TYR A 360 PHE 0.007 0.001 PHE A 288 TRP 0.008 0.001 TRP A 68 HIS 0.005 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9856) covalent geometry : angle 0.51011 / 0.25 (13375) hydrogen bonds : bond 0.03211 / 2.22 ( 588) hydrogen bonds : angle 3.88178 / 2.85 ( 1722) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7771 (m-30) cc_final: 0.7428 (t0) REVERT: A 301 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 412 MET cc_start: 0.7839 (tpp) cc_final: 0.7023 (mmm) REVERT: A 456 MET cc_start: 0.7253 (tpp) cc_final: 0.6733 (mtt) REVERT: A 472 MET cc_start: 0.8553 (tpp) cc_final: 0.8282 (tpt) REVERT: A 482 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8004 (t80) REVERT: A 487 LYS cc_start: 0.9294 (mttt) cc_final: 0.8871 (mtmm) REVERT: A 543 MET cc_start: 0.8420 (mmm) cc_final: 0.8080 (mmm) REVERT: A 708 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8620 (pp) REVERT: A 735 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8069 (mt-10) REVERT: A 958 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7017 (pm20) REVERT: A 968 LYS cc_start: 0.8477 (pttt) cc_final: 0.7337 (mmtm) REVERT: A 970 GLN cc_start: 0.7183 (tt0) cc_final: 0.6442 (tm-30) REVERT: A 977 TYR cc_start: 0.8253 (t80) cc_final: 0.7985 (t80) REVERT: A 1010 MET cc_start: 0.7575 (ttm) cc_final: 0.5866 (tmm) REVERT: B 18 ASP cc_start: 0.8115 (t70) cc_final: 0.7435 (t0) REVERT: B 30 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.8287 (m-70) REVERT: B 36 GLU cc_start: 0.8606 (tp30) cc_final: 0.8383 (tp30) REVERT: B 122 ASN cc_start: 0.9222 (t0) cc_final: 0.9000 (t0) REVERT: B 149 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.8783 (pt) REVERT: B 156 ASN cc_start: 0.8998 (m-40) cc_final: 0.8795 (m-40) REVERT: B 171 ASP cc_start: 0.8966 (m-30) cc_final: 0.8542 (m-30) outliers start: 28 outliers final: 21 residues processed: 120 average time/residue: 0.0826 time to fit residues: 14.7303 Evaluate side-chains 116 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 958 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [116, 28, 3, 36, 27, 104, 34, 108, 65, 47, 107] chunk 116 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** 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 = 0.3430 r_free = 0.3430 target = 0.098317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.079377 restraints weight = 20944.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.082382 restraints weight = 10280.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.084422 restraints weight = 6558.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.085772 restraints weight = 4840.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086490 restraints weight = 3930.081| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9856 Z= 0.117 Angle : 0.528 7.869 13375 Z= 0.263 Chirality : 0.040 0.147 1498 Planarity : 0.004 0.040 1721 Dihedral : 8.284 146.838 1293 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.92 % Allowed : 18.46 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.25), residues: 1182 helix: 2.27 (0.19), residues: 788 sheet: -0.51 (0.75), residues: 53 loop : 0.43 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.010 0.001 TYR A 360 PHE 0.008 0.001 PHE A 538 TRP 0.007 0.001 TRP A 68 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9856) covalent geometry : angle 0.52805 / 0.26 (13375) hydrogen bonds : bond 0.03298 / 2.29 ( 588) hydrogen bonds : angle 3.87069 / 2.85 ( 1722) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7763 (m-30) cc_final: 0.7429 (t0) REVERT: A 100 MET cc_start: 0.8024 (mmm) cc_final: 0.7768 (mmm) REVERT: A 114 ILE cc_start: 0.8970 (tt) cc_final: 0.8752 (tt) REVERT: A 136 TYR cc_start: 0.8381 (m-80) cc_final: 0.8050 (m-80) REVERT: A 412 MET cc_start: 0.7843 (tpp) cc_final: 0.7072 (mmm) REVERT: A 456 MET cc_start: 0.6985 (tpp) cc_final: 0.6669 (ttm) REVERT: A 472 MET cc_start: 0.8539 (tpp) cc_final: 0.8208 (tpt) REVERT: A 482 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.8002 (t80) REVERT: A 487 LYS cc_start: 0.9294 (mttt) cc_final: 0.8875 (mtmm) REVERT: A 543 MET cc_start: 0.8386 (mmm) cc_final: 0.8041 (mmm) REVERT: A 565 MET cc_start: 0.9174 (tpp) cc_final: 0.8971 (mmm) REVERT: A 708 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8632 (pp) REVERT: A 735 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8076 (mt-10) REVERT: A 958 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7006 (pm20) REVERT: A 968 LYS cc_start: 0.8460 (pttt) cc_final: 0.7330 (mmtm) REVERT: A 970 GLN cc_start: 0.7270 (tt0) cc_final: 0.6466 (tm-30) REVERT: A 977 TYR cc_start: 0.8251 (t80) cc_final: 0.7974 (t80) REVERT: A 1010 MET cc_start: 0.7701 (ttm) cc_final: 0.6079 (tmm) REVERT: B 18 ASP cc_start: 0.8099 (t70) cc_final: 0.7419 (t0) REVERT: B 30 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8422 (m-70) REVERT: B 149 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.8543 (pt) REVERT: B 156 ASN cc_start: 0.9015 (m-40) cc_final: 0.8755 (m-40) REVERT: B 171 ASP cc_start: 0.8992 (m-30) cc_final: 0.8528 (m-30) outliers start: 31 outliers final: 21 residues processed: 119 average time/residue: 0.0752 time to fit residues: 13.5564 Evaluate side-chains 117 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 958 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 30 HIS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [28, 89, 9, 15, 92, 19, 2, 88, 20, 60, 110] chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** 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 = 0.3422 r_free = 0.3422 target = 0.097951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.078869 restraints weight = 21087.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.081874 restraints weight = 10377.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.083930 restraints weight = 6614.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.085267 restraints weight = 4885.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.086219 restraints weight = 3975.310| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9856 Z= 0.121 Angle : 0.529 7.667 13375 Z= 0.264 Chirality : 0.040 0.149 1498 Planarity : 0.004 0.040 1721 Dihedral : 8.295 147.216 1293 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.82 % Allowed : 18.83 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.25), residues: 1182 helix: 2.26 (0.19), residues: 785 sheet: -0.49 (0.75), residues: 53 loop : 0.40 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.011 0.001 TYR A 360 PHE 0.007 0.001 PHE A 798 TRP 0.008 0.001 TRP A 145 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 9856) covalent geometry : angle 0.52924 / 0.26 (13375) hydrogen bonds : bond 0.03272 / 2.28 ( 588) hydrogen bonds : angle 3.88132 / 2.85 ( 1722) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8323 (mmm) REVERT: A 87 ASP cc_start: 0.7770 (m-30) cc_final: 0.7432 (t0) REVERT: A 100 MET cc_start: 0.8036 (mmm) cc_final: 0.7697 (mmm) REVERT: A 412 MET cc_start: 0.7837 (tpp) cc_final: 0.7067 (mmm) REVERT: A 472 MET cc_start: 0.8540 (tpp) cc_final: 0.8206 (tpt) REVERT: A 482 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.7987 (t80) REVERT: A 487 LYS cc_start: 0.9316 (mttt) cc_final: 0.8891 (mtmm) REVERT: A 565 MET cc_start: 0.9190 (tpp) cc_final: 0.8980 (mmm) REVERT: A 708 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8633 (pp) REVERT: A 735 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8184 (mt-10) REVERT: A 958 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: A 968 LYS cc_start: 0.8461 (pttt) cc_final: 0.7334 (mmtm) REVERT: A 970 GLN cc_start: 0.7278 (tt0) cc_final: 0.6467 (tm-30) REVERT: A 977 TYR cc_start: 0.8266 (t80) cc_final: 0.7978 (t80) REVERT: A 1010 MET cc_start: 0.7685 (ttm) cc_final: 0.6074 (tmm) REVERT: B 18 ASP cc_start: 0.8111 (t70) cc_final: 0.7438 (t0) REVERT: B 149 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.8507 (pt) REVERT: B 156 ASN cc_start: 0.9032 (m-40) cc_final: 0.8501 (m110) REVERT: B 171 ASP cc_start: 0.9002 (m-30) cc_final: 0.8533 (m-30) outliers start: 30 outliers final: 21 residues processed: 115 average time/residue: 0.0778 time to fit residues: 13.5184 Evaluate side-chains 118 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 958 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [100, 78, 88, 29, 9, 50, 0, 104, 56, 17, 73] chunk 100 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 88 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.097639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078613 restraints weight = 21013.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.081633 restraints weight = 10359.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.083665 restraints weight = 6600.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.085037 restraints weight = 4874.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085953 restraints weight = 3950.140| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9856 Z= 0.124 Angle : 0.537 7.651 13375 Z= 0.268 Chirality : 0.040 0.147 1498 Planarity : 0.004 0.040 1721 Dihedral : 8.304 147.500 1293 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.82 % Allowed : 19.11 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.25), residues: 1182 helix: 2.26 (0.19), residues: 785 sheet: -0.32 (0.78), residues: 48 loop : 0.34 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.011 0.001 TYR A 360 PHE 0.007 0.001 PHE A 798 TRP 0.009 0.001 TRP A 68 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 9856) covalent geometry : angle 0.53658 / 0.27 (13375) hydrogen bonds : bond 0.03357 / 2.33 ( 588) hydrogen bonds : angle 3.88789 / 2.86 ( 1722) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7790 (m-30) cc_final: 0.7452 (t0) REVERT: A 100 MET cc_start: 0.8206 (mmm) cc_final: 0.7956 (mmm) REVERT: A 412 MET cc_start: 0.7839 (tpp) cc_final: 0.7063 (mmm) REVERT: A 472 MET cc_start: 0.8546 (tpp) cc_final: 0.8215 (tpt) REVERT: A 482 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.7985 (t80) REVERT: A 487 LYS cc_start: 0.9319 (mttt) cc_final: 0.8892 (mtmm) REVERT: A 500 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8454 (mm) REVERT: A 671 MET cc_start: 0.8916 (tpp) cc_final: 0.8340 (tpp) REVERT: A 708 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8640 (pp) REVERT: A 735 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 958 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7069 (pm20) REVERT: A 968 LYS cc_start: 0.8453 (pttt) cc_final: 0.7332 (mmtm) REVERT: A 970 GLN cc_start: 0.7279 (tt0) cc_final: 0.6464 (tm-30) REVERT: A 977 TYR cc_start: 0.8299 (t80) cc_final: 0.8021 (t80) REVERT: A 1010 MET cc_start: 0.7698 (ttm) cc_final: 0.6087 (tmm) REVERT: B 18 ASP cc_start: 0.8147 (t70) cc_final: 0.7811 (t0) REVERT: B 36 GLU cc_start: 0.8350 (tp30) cc_final: 0.8046 (tp30) REVERT: B 149 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.8491 (pt) REVERT: B 156 ASN cc_start: 0.9041 (m-40) cc_final: 0.8778 (m-40) REVERT: B 171 ASP cc_start: 0.9011 (m-30) cc_final: 0.8536 (m-30) outliers start: 30 outliers final: 22 residues processed: 115 average time/residue: 0.0768 time to fit residues: 13.4816 Evaluate side-chains 115 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 958 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [55, 44, 114, 88, 13, 92, 30, 54, 103, 22, 78] chunk 55 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** 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 = 0.3400 r_free = 0.3400 target = 0.096671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.077783 restraints weight = 21189.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080762 restraints weight = 10395.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.082761 restraints weight = 6609.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.084056 restraints weight = 4884.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.084970 restraints weight = 3989.121| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9856 Z= 0.138 Angle : 0.560 9.639 13375 Z= 0.278 Chirality : 0.041 0.157 1498 Planarity : 0.004 0.040 1721 Dihedral : 8.299 144.144 1293 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.45 % Allowed : 19.40 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.25), residues: 1182 helix: 2.23 (0.18), residues: 786 sheet: -0.29 (0.76), residues: 49 loop : 0.33 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.013 0.001 TYR A 360 PHE 0.008 0.001 PHE A 538 TRP 0.006 0.001 TRP A 68 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9856) covalent geometry : angle 0.55952 / 0.28 (13375) hydrogen bonds : bond 0.03493 / 2.43 ( 588) hydrogen bonds : angle 3.92239 / 2.89 ( 1722) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7791 (m-30) cc_final: 0.7463 (t0) REVERT: A 100 MET cc_start: 0.8322 (mmm) cc_final: 0.8005 (mmm) REVERT: A 111 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8475 (m) REVERT: A 412 MET cc_start: 0.7861 (tpp) cc_final: 0.7087 (mmm) REVERT: A 472 MET cc_start: 0.8559 (tpp) cc_final: 0.8220 (tpt) REVERT: A 482 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.7988 (t80) REVERT: A 487 LYS cc_start: 0.9324 (mttt) cc_final: 0.8941 (mtmm) REVERT: A 500 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8466 (mm) REVERT: A 671 MET cc_start: 0.8922 (tpp) cc_final: 0.8330 (tpp) REVERT: A 708 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8652 (pp) REVERT: A 735 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8194 (mt-10) REVERT: A 958 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7058 (pm20) REVERT: A 968 LYS cc_start: 0.8449 (pttt) cc_final: 0.7367 (mmtm) REVERT: A 970 GLN cc_start: 0.7312 (tt0) cc_final: 0.6336 (tm-30) REVERT: A 1010 MET cc_start: 0.7725 (ttm) cc_final: 0.6216 (tmm) REVERT: B 18 ASP cc_start: 0.8175 (t70) cc_final: 0.7831 (t0) REVERT: B 36 GLU cc_start: 0.8331 (tp30) cc_final: 0.8027 (tp30) REVERT: B 149 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.8487 (pt) REVERT: B 156 ASN cc_start: 0.9050 (m-40) cc_final: 0.8515 (m110) REVERT: B 171 ASP cc_start: 0.9028 (m-30) cc_final: 0.8549 (m-30) outliers start: 26 outliers final: 20 residues processed: 108 average time/residue: 0.0800 time to fit residues: 13.0264 Evaluate side-chains 112 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 482 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 958 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [5, 54, 100, 101, 85, 104, 94, 34, 3, 108, 80] chunk 5 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 100 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.097208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.078360 restraints weight = 21036.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.081349 restraints weight = 10308.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.083326 restraints weight = 6554.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.084677 restraints weight = 4851.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.085607 restraints weight = 3927.364| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9856 Z= 0.126 Angle : 0.545 7.877 13375 Z= 0.272 Chirality : 0.041 0.150 1498 Planarity : 0.004 0.040 1721 Dihedral : 8.299 142.276 1293 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.54 % Allowed : 19.87 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.25), residues: 1182 helix: 2.20 (0.18), residues: 785 sheet: -0.33 (0.77), residues: 48 loop : 0.33 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.011 0.001 TYR A 360 PHE 0.012 0.001 PHE A 687 TRP 0.009 0.001 TRP A 68 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9856) covalent geometry : angle 0.54474 / 0.27 (13375) hydrogen bonds : bond 0.03404 / 2.37 ( 588) hydrogen bonds : angle 3.91075 / 2.88 ( 1722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1360.42 seconds wall clock time: 24 minutes 17.30 seconds (1457.30 seconds total)