Starting phenix.real_space_refine on Fri May 16 19:22:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dj8_46936/05_2025/9dj8_46936_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dj8_46936/05_2025/9dj8_46936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dj8_46936/05_2025/9dj8_46936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dj8_46936/05_2025/9dj8_46936.map" model { file = "/net/cci-nas-00/data/ceres_data/9dj8_46936/05_2025/9dj8_46936_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dj8_46936/05_2025/9dj8_46936_neut_trim.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1 5.49 5 S 54 5.16 5 C 4826 2.51 5 N 1270 2.21 5 O 1416 1.98 5 H 7277 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14846 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 14720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 14720 Classifications: {'peptide': 931} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 900} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 102 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4821 SG CYS A 301 17.273 35.922 70.950 1.00 1.26 S ATOM 4898 SG CYS A 306 16.341 38.172 73.836 1.00 6.08 S ATOM 4963 SG CYS A 310 19.135 34.916 74.170 1.00 2.03 S ATOM 7720 SG CYS A 487 14.817 48.119 53.359 1.00 8.37 S ATOM 10237 SG CYS A 645 13.344 50.103 56.321 1.00 7.07 S ATOM 10247 SG CYS A 646 13.475 46.185 56.417 1.00 6.84 S Time building chain proxies: 7.49, per 1000 atoms: 0.50 Number of scatterers: 14846 At special positions: 0 Unit cell: (84.48, 96, 137.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 54 16.00 P 1 15.00 O 1416 8.00 N 1270 7.00 C 4826 6.00 H 7277 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " Number of angles added : 6 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1786 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 50.0% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.866A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.676A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.605A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.850A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 removed outlier: 3.556A pdb=" N LEU A 241 " --> pdb=" O TYR A 237 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 4.151A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.646A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.775A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.566A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.509A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.779A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.827A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.993A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.673A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.532A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.662A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.519A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 removed outlier: 3.539A pdb=" N GLN A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.536A pdb=" N TYR A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.510A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 902 removed outlier: 3.997A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.792A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.547A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.401A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.387A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 331 removed outlier: 6.665A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 339 removed outlier: 6.686A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 387 removed outlier: 6.488A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 672 " --> pdb=" O CYS A 669 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 757 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.824A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 891 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: 5.22 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7254 1.03 - 1.23: 113 1.23 - 1.42: 3330 1.42 - 1.62: 4259 1.62 - 1.82: 79 Bond restraints: 15035 Sorted by residual: bond pdb=" C4 AMP G 201 " pdb=" C5 AMP G 201 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C GLY A 203 " pdb=" O GLY A 203 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.12e-02 7.97e+03 2.12e+01 bond pdb=" C5 AMP G 201 " pdb=" C6 AMP G 201 " ideal model delta sigma weight residual 1.490 1.403 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C LEU A 205 " pdb=" O LEU A 205 " ideal model delta sigma weight residual 1.236 1.196 0.039 1.22e-02 6.72e+03 1.05e+01 bond pdb=" C ASP A 825 " pdb=" O ASP A 825 " ideal model delta sigma weight residual 1.235 1.198 0.037 1.22e-02 6.72e+03 9.29e+00 ... (remaining 15030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.27: 26980 14.27 - 28.54: 3 28.54 - 42.81: 1 42.81 - 57.08: 0 57.08 - 71.36: 1 Bond angle restraints: 26985 Sorted by residual: angle pdb=" C SER A 759 " pdb=" N ASP A 760 " pdb=" CA ASP A 760 " ideal model delta sigma weight residual 122.36 162.98 -40.62 1.42e+00 4.96e-01 8.18e+02 angle pdb=" C SER A 759 " pdb=" N ASP A 760 " pdb=" H ASP A 760 " ideal model delta sigma weight residual 123.97 52.61 71.36 3.00e+00 1.11e-01 5.66e+02 angle pdb=" N ASP A 760 " pdb=" CA ASP A 760 " pdb=" CB ASP A 760 " ideal model delta sigma weight residual 111.70 89.70 22.00 1.48e+00 4.57e-01 2.21e+02 angle pdb=" C SER A 759 " pdb=" CA SER A 759 " pdb=" CB SER A 759 " ideal model delta sigma weight residual 112.06 95.53 16.53 1.57e+00 4.06e-01 1.11e+02 angle pdb=" N SER A 759 " pdb=" CA SER A 759 " pdb=" C SER A 759 " ideal model delta sigma weight residual 111.17 124.57 -13.40 1.41e+00 5.03e-01 9.04e+01 ... (remaining 26980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.80: 6984 31.80 - 63.61: 177 63.61 - 95.41: 10 95.41 - 127.22: 0 127.22 - 159.02: 1 Dihedral angle restraints: 7172 sinusoidal: 3740 harmonic: 3432 Sorted by residual: dihedral pdb=" N ASP A 760 " pdb=" C ASP A 760 " pdb=" CA ASP A 760 " pdb=" CB ASP A 760 " ideal model delta harmonic sigma weight residual 122.80 95.41 27.39 0 2.50e+00 1.60e-01 1.20e+02 dihedral pdb=" C2' AMP G 201 " pdb=" C1' AMP G 201 " pdb=" N9 AMP G 201 " pdb=" C4 AMP G 201 " ideal model delta sinusoidal sigma weight residual 91.55 -67.47 159.02 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C ASP A 760 " pdb=" N ASP A 760 " pdb=" CA ASP A 760 " pdb=" CB ASP A 760 " ideal model delta harmonic sigma weight residual -122.60 -107.31 -15.29 0 2.50e+00 1.60e-01 3.74e+01 ... (remaining 7169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1127 0.121 - 0.242: 21 0.242 - 0.362: 0 0.362 - 0.483: 1 0.483 - 0.604: 1 Chirality restraints: 1150 Sorted by residual: chirality pdb=" CA ASP A 760 " pdb=" N ASP A 760 " pdb=" C ASP A 760 " pdb=" CB ASP A 760 " both_signs ideal model delta sigma weight residual False 2.51 3.11 -0.60 2.00e-01 2.50e+01 9.12e+00 chirality pdb=" CA VAL A 844 " pdb=" N VAL A 844 " pdb=" C VAL A 844 " pdb=" CB VAL A 844 " both_signs ideal model delta sigma weight residual False 2.44 2.82 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA THR A 76 " pdb=" N THR A 76 " pdb=" C THR A 76 " pdb=" CB THR A 76 " both_signs ideal model delta sigma weight residual False 2.53 2.76 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1147 not shown) Planarity restraints: 2259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 74 " -0.210 9.50e-02 1.11e+02 3.35e-01 2.43e+03 pdb=" NE ARG A 74 " 0.244 2.00e-02 2.50e+03 pdb=" CZ ARG A 74 " 0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG A 74 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 74 " -0.046 2.00e-02 2.50e+03 pdb="HH11 ARG A 74 " -0.700 2.00e-02 2.50e+03 pdb="HH12 ARG A 74 " 0.625 2.00e-02 2.50e+03 pdb="HH21 ARG A 74 " -0.146 2.00e-02 2.50e+03 pdb="HH22 ARG A 74 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 822 " -0.230 2.00e-02 2.50e+03 2.76e-01 1.14e+03 pdb=" CD GLN A 822 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN A 822 " 0.228 2.00e-02 2.50e+03 pdb=" NE2 GLN A 822 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 822 " -0.422 2.00e-02 2.50e+03 pdb="HE22 GLN A 822 " 0.417 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 76 " -0.044 2.00e-02 2.50e+03 8.35e-02 6.97e+01 pdb=" N PHE A 77 " 0.144 2.00e-02 2.50e+03 pdb=" CA PHE A 77 " -0.038 2.00e-02 2.50e+03 pdb=" H PHE A 77 " -0.062 2.00e-02 2.50e+03 ... (remaining 2256 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.79: 20 1.79 - 2.49: 9798 2.49 - 3.20: 41618 3.20 - 3.90: 56040 3.90 - 4.60: 89220 Nonbonded interactions: 196696 Sorted by model distance: nonbonded pdb=" O ASP A 845 " pdb="HG12 VAL A 848 " model vdw 1.089 2.620 nonbonded pdb=" O SER A 759 " pdb=" HG SER A 759 " model vdw 1.160 2.450 nonbonded pdb=" O SER A 759 " pdb=" H ASP A 760 " model vdw 1.485 1.960 nonbonded pdb="HH12 ARG A 18 " pdb=" OD1 ASP A 63 " model vdw 1.486 2.450 nonbonded pdb=" OD1 ASP A 846 " pdb=" H ILE A 847 " model vdw 1.520 2.450 ... (remaining 196691 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.440 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: 0.260 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.007 0.253 7767 Z= 0.310 Angle : 0.930 40.615 10539 Z= 0.566 Chirality : 0.052 0.604 1150 Planarity : 0.009 0.239 1354 Dihedral : 14.203 159.019 2783 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.66 % Allowed : 7.97 % Favored : 89.37 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.25), residues: 934 helix: -0.64 (0.25), residues: 399 sheet: -0.97 (0.42), residues: 124 loop : -1.98 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 916 HIS 0.004 0.001 HIS A 642 PHE 0.025 0.002 PHE A 652 TYR 0.019 0.003 TYR A 80 ARG 0.005 0.001 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.23607 ( 329) hydrogen bonds : angle 6.37272 ( 891) metal coordination : bond 0.10552 ( 8) metal coordination : angle 7.69042 ( 6) covalent geometry : bond 0.00634 ( 7758) covalent geometry : angle 0.91221 (10533) Misc. bond : bond 0.05180 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 5 residues processed: 65 average time/residue: 2.7240 time to fit residues: 188.4135 Evaluate side-chains 42 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.054760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.042884 restraints weight = 60296.454| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 2.55 r_work: 0.2615 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7767 Z= 0.141 Angle : 0.528 12.675 10539 Z= 0.296 Chirality : 0.041 0.141 1150 Planarity : 0.004 0.047 1354 Dihedral : 7.579 154.530 1053 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.69 % Allowed : 9.18 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.26), residues: 934 helix: 0.59 (0.27), residues: 395 sheet: -0.48 (0.45), residues: 116 loop : -1.81 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.003 0.001 HIS A 309 PHE 0.013 0.001 PHE A 753 TYR 0.013 0.001 TYR A 80 ARG 0.006 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.05789 ( 329) hydrogen bonds : angle 4.29153 ( 891) metal coordination : bond 0.00472 ( 8) metal coordination : angle 1.16268 ( 6) covalent geometry : bond 0.00319 ( 7758) covalent geometry : angle 0.52703 (10533) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 1.182 Fit side-chains REVERT: A 681 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8548 (t) REVERT: A 902 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7976 (ptp) outliers start: 14 outliers final: 5 residues processed: 50 average time/residue: 1.9657 time to fit residues: 106.5333 Evaluate side-chains 43 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 902 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.053598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.041583 restraints weight = 60205.581| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 2.60 r_work: 0.2572 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7767 Z= 0.174 Angle : 0.516 12.111 10539 Z= 0.289 Chirality : 0.041 0.137 1150 Planarity : 0.004 0.045 1354 Dihedral : 7.301 153.228 1050 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.09 % Allowed : 10.27 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.27), residues: 934 helix: 0.99 (0.27), residues: 394 sheet: -0.44 (0.46), residues: 116 loop : -1.78 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.003 0.001 HIS A 256 PHE 0.013 0.001 PHE A 741 TYR 0.014 0.001 TYR A 80 ARG 0.007 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.05893 ( 329) hydrogen bonds : angle 4.10607 ( 891) metal coordination : bond 0.00978 ( 8) metal coordination : angle 1.67354 ( 6) covalent geometry : bond 0.00412 ( 7758) covalent geometry : angle 0.51484 (10533) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 45 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.8072 (ptt) cc_final: 0.7744 (ptp) outliers start: 9 outliers final: 6 residues processed: 45 average time/residue: 2.1342 time to fit residues: 103.9469 Evaluate side-chains 40 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.053263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.041588 restraints weight = 60673.922| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.54 r_work: 0.2586 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 7767 Z= 0.201 Angle : 0.522 11.999 10539 Z= 0.292 Chirality : 0.042 0.135 1150 Planarity : 0.004 0.043 1354 Dihedral : 7.222 151.904 1049 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.33 % Allowed : 10.27 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.27), residues: 934 helix: 0.99 (0.27), residues: 401 sheet: -0.42 (0.46), residues: 116 loop : -1.80 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.002 0.001 HIS A 882 PHE 0.013 0.001 PHE A 741 TYR 0.014 0.001 TYR A 80 ARG 0.009 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.06030 ( 329) hydrogen bonds : angle 4.10897 ( 891) metal coordination : bond 0.01020 ( 8) metal coordination : angle 1.69087 ( 6) covalent geometry : bond 0.00478 ( 7758) covalent geometry : angle 0.52024 (10533) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.7965 (ptt) cc_final: 0.7670 (ptp) outliers start: 11 outliers final: 6 residues processed: 45 average time/residue: 2.3352 time to fit residues: 113.2054 Evaluate side-chains 41 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.054481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.042481 restraints weight = 59782.063| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 2.62 r_work: 0.2593 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7767 Z= 0.121 Angle : 0.472 12.107 10539 Z= 0.262 Chirality : 0.039 0.137 1150 Planarity : 0.004 0.049 1354 Dihedral : 6.993 150.206 1049 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.45 % Allowed : 10.39 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.28), residues: 934 helix: 1.24 (0.28), residues: 400 sheet: -0.29 (0.46), residues: 116 loop : -1.69 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.002 0.001 HIS A 309 PHE 0.012 0.001 PHE A 753 TYR 0.011 0.001 TYR A 80 ARG 0.009 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 329) hydrogen bonds : angle 3.85545 ( 891) metal coordination : bond 0.00671 ( 8) metal coordination : angle 1.16350 ( 6) covalent geometry : bond 0.00278 ( 7758) covalent geometry : angle 0.47159 (10533) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 48 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.7713 (ptt) cc_final: 0.7441 (ptp) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 2.2220 time to fit residues: 112.8967 Evaluate side-chains 41 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.054344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.042379 restraints weight = 59657.594| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 2.60 r_work: 0.2592 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7767 Z= 0.140 Angle : 0.481 12.036 10539 Z= 0.266 Chirality : 0.040 0.135 1150 Planarity : 0.004 0.053 1354 Dihedral : 6.947 150.082 1049 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.09 % Allowed : 11.23 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.28), residues: 934 helix: 1.30 (0.28), residues: 400 sheet: -0.22 (0.46), residues: 116 loop : -1.64 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.002 0.001 HIS A 256 PHE 0.012 0.001 PHE A 753 TYR 0.012 0.001 TYR A 80 ARG 0.008 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 329) hydrogen bonds : angle 3.86045 ( 891) metal coordination : bond 0.00762 ( 8) metal coordination : angle 1.23925 ( 6) covalent geometry : bond 0.00327 ( 7758) covalent geometry : angle 0.47984 (10533) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 44 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.7451 (ptt) cc_final: 0.7218 (ptp) outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 2.0882 time to fit residues: 97.4965 Evaluate side-chains 42 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.053335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.041377 restraints weight = 59809.732| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 2.60 r_work: 0.2566 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 7767 Z= 0.202 Angle : 0.514 11.847 10539 Z= 0.286 Chirality : 0.042 0.134 1150 Planarity : 0.004 0.057 1354 Dihedral : 7.042 150.176 1049 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.85 % Allowed : 11.59 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.27), residues: 934 helix: 1.22 (0.27), residues: 401 sheet: -0.22 (0.46), residues: 116 loop : -1.70 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.002 0.001 HIS A 256 PHE 0.013 0.001 PHE A 753 TYR 0.014 0.001 TYR A 80 ARG 0.009 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.05770 ( 329) hydrogen bonds : angle 3.96522 ( 891) metal coordination : bond 0.00945 ( 8) metal coordination : angle 1.62424 ( 6) covalent geometry : bond 0.00481 ( 7758) covalent geometry : angle 0.51283 (10533) Misc. bond : bond 0.00046 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 43 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 1.052 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 43 average time/residue: 2.2398 time to fit residues: 103.8160 Evaluate side-chains 41 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.054403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.042333 restraints weight = 59697.441| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 2.63 r_work: 0.2600 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7767 Z= 0.125 Angle : 0.485 12.039 10539 Z= 0.266 Chirality : 0.039 0.137 1150 Planarity : 0.004 0.062 1354 Dihedral : 6.885 149.252 1049 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.97 % Allowed : 11.11 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.28), residues: 934 helix: 1.46 (0.28), residues: 395 sheet: -0.14 (0.46), residues: 116 loop : -1.54 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.002 0.001 HIS A 928 PHE 0.012 0.001 PHE A 753 TYR 0.011 0.001 TYR A 80 ARG 0.009 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 329) hydrogen bonds : angle 3.81897 ( 891) metal coordination : bond 0.00661 ( 8) metal coordination : angle 1.17808 ( 6) covalent geometry : bond 0.00290 ( 7758) covalent geometry : angle 0.48448 (10533) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 43 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 1.164 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 2.2594 time to fit residues: 102.2364 Evaluate side-chains 40 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 40 optimal weight: 0.0040 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.055209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.043188 restraints weight = 59198.513| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.62 r_work: 0.2617 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7767 Z= 0.102 Angle : 0.458 12.119 10539 Z= 0.251 Chirality : 0.039 0.138 1150 Planarity : 0.003 0.038 1354 Dihedral : 6.542 148.143 1047 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.72 % Allowed : 11.35 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.28), residues: 934 helix: 1.59 (0.28), residues: 396 sheet: 0.04 (0.47), residues: 111 loop : -1.47 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.002 0.000 HIS A 898 PHE 0.011 0.001 PHE A 753 TYR 0.010 0.001 TYR A 80 ARG 0.004 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 329) hydrogen bonds : angle 3.70659 ( 891) metal coordination : bond 0.00518 ( 8) metal coordination : angle 1.00164 ( 6) covalent geometry : bond 0.00230 ( 7758) covalent geometry : angle 0.45741 (10533) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 43 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 1.113 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 2.5593 time to fit residues: 114.9228 Evaluate side-chains 40 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.053930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.041917 restraints weight = 59992.762| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 2.61 r_work: 0.2589 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7767 Z= 0.159 Angle : 0.508 11.971 10539 Z= 0.278 Chirality : 0.040 0.133 1150 Planarity : 0.004 0.104 1354 Dihedral : 6.685 149.244 1047 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.48 % Allowed : 11.84 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.28), residues: 934 helix: 1.51 (0.28), residues: 395 sheet: 0.03 (0.47), residues: 111 loop : -1.49 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.002 0.001 HIS A 309 PHE 0.013 0.001 PHE A 753 TYR 0.012 0.001 TYR A 80 ARG 0.013 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.05138 ( 329) hydrogen bonds : angle 3.85499 ( 891) metal coordination : bond 0.00728 ( 8) metal coordination : angle 1.46267 ( 6) covalent geometry : bond 0.00377 ( 7758) covalent geometry : angle 0.50646 (10533) Misc. bond : bond 0.00039 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 849 is missing expected H atoms. Skipping. Evaluate side-chains 39 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 1.053 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 39 average time/residue: 2.3773 time to fit residues: 99.6703 Evaluate side-chains 39 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 760 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.054469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.042392 restraints weight = 60174.710| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 2.64 r_work: 0.2593 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7767 Z= 0.128 Angle : 0.474 12.024 10539 Z= 0.262 Chirality : 0.040 0.136 1150 Planarity : 0.004 0.093 1354 Dihedral : 6.633 148.872 1047 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.48 % Allowed : 11.84 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.28), residues: 934 helix: 1.56 (0.28), residues: 395 sheet: 0.05 (0.46), residues: 111 loop : -1.45 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.002 0.000 HIS A 309 PHE 0.012 0.001 PHE A 753 TYR 0.011 0.001 TYR A 80 ARG 0.015 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 329) hydrogen bonds : angle 3.79319 ( 891) metal coordination : bond 0.00644 ( 8) metal coordination : angle 1.20810 ( 6) covalent geometry : bond 0.00298 ( 7758) covalent geometry : angle 0.47291 (10533) Misc. bond : bond 0.00028 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8706.28 seconds wall clock time: 149 minutes 53.26 seconds (8993.26 seconds total)