Starting phenix.real_space_refine on Fri Jun 13 07:12:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dj8_46936/06_2025/9dj8_46936_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dj8_46936/06_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_46936/06_2025/9dj8_46936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dj8_46936/06_2025/9dj8_46936.map" model { file = "/net/cci-nas-00/data/ceres_data/9dj8_46936/06_2025/9dj8_46936_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dj8_46936/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 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: 9.03, per 1000 atoms: 0.61 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: 5.10 Conformation dependent library (CDL) restraints added in 1.0 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: 1.51 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: 5.60 Time building geometry restraints manager: 5.98 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: 1126 0.121 - 0.242: 22 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: 142.490 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: 0.270 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 43.810 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 202.490 ------------------------------------------------------------------------------- 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= 0.311 Angle : 0.944 40.615 10539 Z= 0.569 Chirality : 0.053 0.604 1150 Planarity : 0.009 0.239 1354 Dihedral : 14.196 159.019 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 0.00636 ( 7758) covalent geometry : angle 0.92606 (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 : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 5 residues processed: 65 average time/residue: 2.8254 time to fit residues: 194.8667 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 : 1.212 ------------------------------------------------------------------------------- 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: 0.0970 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3002 r_free = 0.3002 target = 0.055061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.043187 restraints weight = 60204.401| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.54 r_work: 0.2622 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1421 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= 0.131 Angle : 0.529 12.908 10539 Z= 0.294 Chirality : 0.041 0.141 1150 Planarity : 0.004 0.047 1354 Dihedral : 7.207 145.027 1053 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.45 % Allowed : 9.42 % 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: -0.88 (0.26), residues: 934 helix: 0.61 (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 0.011 0.001 TRP A 916 HIS 0.003 0.001 HIS A 309 PHE 0.013 0.001 PHE A 753 TYR 0.012 0.001 TYR A 80 ARG 0.006 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.05675 ( 329) hydrogen bonds : angle 4.28245 ( 891) metal coordination : bond 0.00654 ( 8) metal coordination : angle 1.19795 ( 6) covalent geometry : bond 0.00291 ( 7758) covalent geometry : angle 0.52812 (10533) Misc. bond : bond 0.00017 ( 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 51 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 1.330 Fit side-chains REVERT: A 681 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8471 (t) REVERT: A 731 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9222 (mp) REVERT: A 876 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8653 (mt-10) REVERT: A 902 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7980 (ptp) outliers start: 12 outliers final: 4 residues processed: 48 average time/residue: 2.1043 time to fit residues: 109.7844 Evaluate side-chains 44 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 681 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 876 GLU 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: 1.9990 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 909 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 = 0.2945 r_free = 0.2945 target = 0.053201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.041108 restraints weight = 60374.179| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 2.62 r_work: 0.2560 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1596 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= 0.198 Angle : 0.538 12.037 10539 Z= 0.299 Chirality : 0.042 0.137 1150 Planarity : 0.004 0.045 1354 Dihedral : 6.962 144.602 1050 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.45 % Allowed : 10.14 % 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: -0.65 (0.27), residues: 934 helix: 0.94 (0.27), residues: 394 sheet: -0.47 (0.46), residues: 116 loop : -1.78 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.003 0.001 HIS A 256 PHE 0.014 0.001 PHE A 741 TYR 0.014 0.001 TYR A 80 ARG 0.006 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.06257 ( 329) hydrogen bonds : angle 4.14911 ( 891) metal coordination : bond 0.01116 ( 8) metal coordination : angle 1.81696 ( 6) covalent geometry : bond 0.00474 ( 7758) covalent geometry : angle 0.53598 (10533) Misc. bond : bond 0.00025 ( 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 48 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 790 ASN cc_start: 0.9296 (OUTLIER) cc_final: 0.9095 (t160) REVERT: A 902 MET cc_start: 0.8083 (ptt) cc_final: 0.7748 (ptp) outliers start: 12 outliers final: 6 residues processed: 48 average time/residue: 2.4496 time to fit residues: 126.8821 Evaluate side-chains 41 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 790 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 68 optimal weight: 1.9990 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: 0.6980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.2971 r_free = 0.2971 target = 0.053391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.041587 restraints weight = 60660.052| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 2.56 r_work: 0.2581 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1818 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= 0.195 Angle : 0.526 11.905 10539 Z= 0.292 Chirality : 0.042 0.135 1150 Planarity : 0.004 0.042 1354 Dihedral : 6.779 140.258 1049 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.45 % Allowed : 10.14 % 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: -0.54 (0.27), residues: 934 helix: 1.10 (0.27), residues: 395 sheet: -0.45 (0.46), residues: 116 loop : -1.79 (0.27), residues: 423 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 0.007 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.05848 ( 329) hydrogen bonds : angle 4.09046 ( 891) metal coordination : bond 0.00903 ( 8) metal coordination : angle 1.61484 ( 6) covalent geometry : bond 0.00462 ( 7758) covalent geometry : angle 0.52466 (10533) Misc. bond : bond 0.00036 ( 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 47 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.7958 (ptt) cc_final: 0.7661 (ptp) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 2.1899 time to fit residues: 111.0514 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 : 1.143 ------------------------------------------------------------------------------- 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 760 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 82 optimal weight: 0.0570 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3028 r_free = 0.3028 target = 0.055719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.044056 restraints weight = 59585.641| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.54 r_work: 0.2660 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7767 Z= 0.095 Angle : 0.460 12.155 10539 Z= 0.251 Chirality : 0.039 0.139 1150 Planarity : 0.003 0.044 1354 Dihedral : 6.341 135.407 1049 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.21 % Allowed : 10.87 % 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: -0.21 (0.28), residues: 934 helix: 1.32 (0.28), residues: 402 sheet: -0.25 (0.46), residues: 116 loop : -1.63 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.002 0.000 HIS A 928 PHE 0.012 0.001 PHE A 753 TYR 0.009 0.001 TYR A 831 ARG 0.009 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 329) hydrogen bonds : angle 3.75237 ( 891) metal coordination : bond 0.00460 ( 8) metal coordination : angle 0.99003 ( 6) covalent geometry : bond 0.00208 ( 7758) covalent geometry : angle 0.45917 (10533) Misc. bond : bond 0.00016 ( 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 44 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 43 average time/residue: 2.7425 time to fit residues: 127.3360 Evaluate side-chains 39 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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: 0.9980 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.2997 r_free = 0.2997 target = 0.054345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.042494 restraints weight = 60254.653| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.55 r_work: 0.2618 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7767 Z= 0.157 Angle : 0.492 11.934 10539 Z= 0.270 Chirality : 0.041 0.134 1150 Planarity : 0.004 0.052 1354 Dihedral : 6.415 136.729 1049 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.85 % Allowed : 11.35 % Favored : 87.80 % 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: -0.20 (0.28), residues: 934 helix: 1.35 (0.28), residues: 400 sheet: -0.27 (0.45), residues: 116 loop : -1.61 (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 0.05102 ( 329) hydrogen bonds : angle 3.85947 ( 891) metal coordination : bond 0.00755 ( 8) metal coordination : angle 1.36499 ( 6) covalent geometry : bond 0.00371 ( 7758) covalent geometry : angle 0.49075 (10533) Misc. bond : bond 0.00028 ( 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 42 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 902 MET cc_start: 0.7482 (ptt) cc_final: 0.7277 (ptp) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 2.1567 time to fit residues: 96.1223 Evaluate side-chains 38 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 35 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.2965 r_free = 0.2965 target = 0.053811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.041754 restraints weight = 60103.605| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.62 r_work: 0.2581 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7767 Z= 0.159 Angle : 0.496 11.917 10539 Z= 0.272 Chirality : 0.041 0.134 1150 Planarity : 0.004 0.057 1354 Dihedral : 6.418 135.866 1049 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.97 % Allowed : 11.35 % 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: -0.18 (0.28), residues: 934 helix: 1.35 (0.28), residues: 400 sheet: -0.22 (0.45), residues: 116 loop : -1.60 (0.28), residues: 418 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 0.009 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.05153 ( 329) hydrogen bonds : angle 3.85723 ( 891) metal coordination : bond 0.00778 ( 8) metal coordination : angle 1.45652 ( 6) covalent geometry : bond 0.00375 ( 7758) covalent geometry : angle 0.49460 (10533) Misc. bond : bond 0.00032 ( 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 42 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 1.345 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 2.8663 time to fit residues: 128.8104 Evaluate side-chains 38 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 51 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- 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 = 0.2984 r_free = 0.2984 target = 0.054598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.042463 restraints weight = 59598.204| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.64 r_work: 0.2596 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2195 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= 0.121 Angle : 0.485 12.025 10539 Z= 0.264 Chirality : 0.039 0.136 1150 Planarity : 0.003 0.038 1354 Dihedral : 6.065 134.226 1047 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.97 % Allowed : 11.23 % Favored : 87.80 % 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: -0.03 (0.28), residues: 934 helix: 1.48 (0.28), residues: 397 sheet: -0.17 (0.45), residues: 116 loop : -1.49 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.002 0.000 HIS A 599 PHE 0.012 0.001 PHE A 753 TYR 0.011 0.001 TYR A 80 ARG 0.003 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 329) hydrogen bonds : angle 3.76817 ( 891) metal coordination : bond 0.00619 ( 8) metal coordination : angle 1.17088 ( 6) covalent geometry : bond 0.00282 ( 7758) covalent geometry : angle 0.48460 (10533) Misc. bond : bond 0.00023 ( 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 42 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 3.099 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8266 (mtp) REVERT: A 902 MET cc_start: 0.7800 (mtm) cc_final: 0.7583 (mtm) outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 3.2261 time to fit residues: 143.6444 Evaluate side-chains 38 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 110 MET 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: 0.9980 chunk 75 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 40 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.2991 r_free = 0.2991 target = 0.054875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.042793 restraints weight = 59232.336| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.62 r_work: 0.2615 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2324 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= 0.110 Angle : 0.467 12.038 10539 Z= 0.255 Chirality : 0.039 0.136 1150 Planarity : 0.004 0.103 1354 Dihedral : 5.978 132.552 1047 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.60 % Allowed : 11.71 % 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: 0.09 (0.28), residues: 934 helix: 1.57 (0.28), residues: 397 sheet: 0.02 (0.46), residues: 111 loop : -1.45 (0.28), residues: 426 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 0.014 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 329) hydrogen bonds : angle 3.69685 ( 891) metal coordination : bond 0.00559 ( 8) metal coordination : angle 1.10397 ( 6) covalent geometry : bond 0.00252 ( 7758) covalent geometry : angle 0.46600 (10533) Misc. bond : bond 0.00021 ( 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 37 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8289 (mtp) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 2.0894 time to fit residues: 81.9001 Evaluate side-chains 37 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 110 MET 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: 0.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.2985 r_free = 0.2985 target = 0.054658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.042576 restraints weight = 59608.856| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.62 r_work: 0.2601 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2317 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= 0.122 Angle : 0.476 12.030 10539 Z= 0.260 Chirality : 0.040 0.135 1150 Planarity : 0.004 0.088 1354 Dihedral : 5.970 132.164 1047 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.97 % Allowed : 11.35 % 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: 0.10 (0.28), residues: 934 helix: 1.58 (0.28), residues: 397 sheet: 0.04 (0.46), residues: 111 loop : -1.45 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.003 0.001 HIS A 898 PHE 0.012 0.001 PHE A 753 TYR 0.011 0.001 TYR A 80 ARG 0.013 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 329) hydrogen bonds : angle 3.74319 ( 891) metal coordination : bond 0.00627 ( 8) metal coordination : angle 1.22532 ( 6) covalent geometry : bond 0.00283 ( 7758) covalent geometry : angle 0.47568 (10533) Misc. bond : bond 0.00024 ( 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 40 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 1.194 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 39 average time/residue: 2.1305 time to fit residues: 91.5203 Evaluate side-chains 37 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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 731 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: 1.9990 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: 0.6980 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.2972 r_free = 0.2972 target = 0.054111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.042036 restraints weight = 60242.016| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.64 r_work: 0.2584 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2284 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= 0.146 Angle : 0.486 11.939 10539 Z= 0.267 Chirality : 0.040 0.133 1150 Planarity : 0.004 0.089 1354 Dihedral : 6.046 132.853 1047 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.60 % Allowed : 11.71 % 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: 1.58 (0.28), residues: 395 sheet: 0.03 (0.46), residues: 111 loop : -1.46 (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 898 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 0.04906 ( 329) hydrogen bonds : angle 3.79370 ( 891) metal coordination : bond 0.00758 ( 8) metal coordination : angle 1.44956 ( 6) covalent geometry : bond 0.00344 ( 7758) covalent geometry : angle 0.48514 (10533) Misc. bond : bond 0.00029 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10776.70 seconds wall clock time: 191 minutes 21.97 seconds (11481.97 seconds total)