Starting phenix.real_space_refine on Thu Jul 2 07:34:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gsy_51558/07_2026/9gsy_51558.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gsy_51558/07_2026/9gsy_51558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gsy_51558/07_2026/9gsy_51558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gsy_51558/07_2026/9gsy_51558.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gsy_51558/07_2026/9gsy_51558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gsy_51558/07_2026/9gsy_51558.map" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.081 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: 8 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 47 5.16 5 Be 1 3.05 5 C 4703 2.51 5 N 1231 2.21 5 O 1364 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7353 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7309 Classifications: {'peptide': 941} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 895} Chain breaks: 3 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 1, 'BEF': 1, 'KXP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'KXP:plan-1': 1, 'KXP:plan-3': 1, 'KXP:plan-4': 1, 'KXP:plan-5': 1, 'KXP:plan-6': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 1.58, per 1000 atoms: 0.21 Number of scatterers: 7353 At special positions: 0 Unit cell: (90.09, 140.14, 89.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 47 16.00 P 3 15.00 Mg 1 11.99 F 3 9.00 O 1364 8.00 N 1231 7.00 C 4703 6.00 Be 1 4.00 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: 0.47 Conformation dependent library (CDL) restraints added in 515.1 milliseconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 52.7% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.524A pdb=" N LEU A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 50 removed outlier: 4.226A pdb=" N VAL A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 151 through 184 removed outlier: 4.113A pdb=" N ALA A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN A 183 " --> pdb=" O PHE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.595A pdb=" N ILE A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 379 removed outlier: 3.522A pdb=" N LEU A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 378 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 410 removed outlier: 3.747A pdb=" N TYR A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 395 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 487 through 501 removed outlier: 4.341A pdb=" N GLU A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.863A pdb=" N VAL A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'A' and resid 607 through 622 Proline residue: A 618 - end of helix Processing helix chain 'A' and resid 644 through 649 removed outlier: 4.370A pdb=" N ILE A 648 " --> pdb=" O ASN A 644 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 644 through 649' Processing helix chain 'A' and resid 667 through 678 removed outlier: 3.521A pdb=" N ARG A 673 " --> pdb=" O PRO A 669 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 677 " --> pdb=" O ARG A 673 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.694A pdb=" N LYS A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 722 removed outlier: 3.526A pdb=" N ILE A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 722 " --> pdb=" O ASN A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 737 removed outlier: 3.707A pdb=" N ILE A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 760 removed outlier: 3.531A pdb=" N ILE A 759 " --> pdb=" O VAL A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 786 removed outlier: 3.523A pdb=" N LYS A 785 " --> pdb=" O PRO A 781 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 803 Processing helix chain 'A' and resid 814 through 854 removed outlier: 4.017A pdb=" N LYS A 818 " --> pdb=" O SER A 814 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 839 " --> pdb=" O GLN A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 870 removed outlier: 3.645A pdb=" N TRP A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 881 removed outlier: 3.501A pdb=" N THR A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 removed outlier: 3.563A pdb=" N LEU A 891 " --> pdb=" O THR A 888 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 892 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 927 removed outlier: 3.884A pdb=" N TYR A 916 " --> pdb=" O GLY A 912 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 920 " --> pdb=" O TYR A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 947 through 966 removed outlier: 3.651A pdb=" N THR A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 953 " --> pdb=" O HIS A 949 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 961 " --> pdb=" O PHE A 957 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 963 " --> pdb=" O MET A 959 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1004 removed outlier: 3.579A pdb=" N CYS A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1039 removed outlier: 4.198A pdb=" N GLU A1029 " --> pdb=" O ILE A1025 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A1035 " --> pdb=" O VAL A1031 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A1039 " --> pdb=" O VAL A1035 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.641A pdb=" N VAL A 194 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 203 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 192 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR A 193 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE A 213 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 230 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A 272 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE A 228 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 250 removed outlier: 3.949A pdb=" N LEU A 234 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS A 235 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS A 263 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 434 through 436 removed outlier: 6.412A pdb=" N GLY A 789 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU A 808 " --> pdb=" O GLY A 789 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA A 791 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 770 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N PHE A 790 " --> pdb=" O VAL A 770 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL A 772 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N MET A 792 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLY A 774 " --> pdb=" O MET A 792 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA A 450 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR A 773 " --> pdb=" O ALA A 450 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N CYS A 452 " --> pdb=" O THR A 773 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE A 451 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL A 685 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER A 453 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG A 741 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU A 710 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL A 742 " --> pdb=" O LEU A 710 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.718A pdb=" N VAL A 471 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL A 466 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU A 661 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN A 468 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A 629 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL A 657 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A 627 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY A 659 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG A 625 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 581 " --> pdb=" O CYS A 628 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 553 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.718A pdb=" N VAL A 471 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL A 466 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU A 661 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN A 468 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N CYS A 654 " --> pdb=" O CYS A 591 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 593 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N CYS A 656 " --> pdb=" O ILE A 593 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 507 through 508 removed outlier: 3.556A pdb=" N LEU A 508 " --> pdb=" O ARG A 518 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 1029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1216 1.31 - 1.44: 1793 1.44 - 1.56: 4396 1.56 - 1.69: 5 1.69 - 1.81: 74 Bond restraints: 7484 Sorted by residual: bond pdb=" F2 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.566 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" O41 KXP A1303 " pdb=" P42 KXP A1303 " ideal model delta sigma weight residual 1.725 1.648 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O36 KXP A1303 " pdb=" P37 KXP A1303 " ideal model delta sigma weight residual 1.722 1.647 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C18 KXP A1303 " pdb=" O20 KXP A1303 " ideal model delta sigma weight residual 1.323 1.398 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" F3 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.549 -0.073 2.00e-02 2.50e+03 1.32e+01 ... (remaining 7479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 10099 3.60 - 7.19: 39 7.19 - 10.79: 5 10.79 - 14.39: 1 14.39 - 17.98: 2 Bond angle restraints: 10146 Sorted by residual: angle pdb=" O24 KXP A1303 " pdb=" P25 KXP A1303 " pdb=" O28 KXP A1303 " ideal model delta sigma weight residual 90.95 108.93 -17.98 3.00e+00 1.11e-01 3.59e+01 angle pdb=" F2 BEF A1301 " pdb="BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 119.96 105.24 14.72 3.00e+00 1.11e-01 2.41e+01 angle pdb=" F1 BEF A1301 " pdb="BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 120.12 109.23 10.89 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C1 KXP A1303 " pdb=" C18 KXP A1303 " pdb=" O20 KXP A1303 " ideal model delta sigma weight residual 110.71 120.80 -10.09 3.00e+00 1.11e-01 1.13e+01 angle pdb=" O26 KXP A1303 " pdb=" P25 KXP A1303 " pdb=" O27 KXP A1303 " ideal model delta sigma weight residual 119.47 109.45 10.02 3.00e+00 1.11e-01 1.11e+01 ... (remaining 10141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.12: 4417 27.12 - 54.24: 150 54.24 - 81.36: 14 81.36 - 108.47: 0 108.47 - 135.59: 1 Dihedral angle restraints: 4582 sinusoidal: 1876 harmonic: 2706 Sorted by residual: dihedral pdb=" O20 KXP A1303 " pdb=" C21 KXP A1303 " pdb=" C22 KXP A1303 " pdb=" O48 KXP A1303 " ideal model delta sinusoidal sigma weight residual 51.71 -83.88 135.59 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" CA MET A 570 " pdb=" C MET A 570 " pdb=" N PRO A 571 " pdb=" CA PRO A 571 " ideal model delta harmonic sigma weight residual 180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASP A 662 " pdb=" C ASP A 662 " pdb=" N PRO A 663 " pdb=" CA PRO A 663 " ideal model delta harmonic sigma weight residual -180.00 -163.19 -16.81 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 4579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 643 0.027 - 0.053: 347 0.053 - 0.079: 127 0.079 - 0.106: 55 0.106 - 0.132: 30 Chirality restraints: 1202 Sorted by residual: chirality pdb=" CA THR A 53 " pdb=" N THR A 53 " pdb=" C THR A 53 " pdb=" CB THR A 53 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ASP A 811 " pdb=" N ASP A 811 " pdb=" C ASP A 811 " pdb=" CB ASP A 811 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA TRP A 737 " pdb=" N TRP A 737 " pdb=" C TRP A 737 " pdb=" CB TRP A 737 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1199 not shown) Planarity restraints: 1277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 607 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C ASP A 607 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP A 607 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 608 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 546 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A 547 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 547 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 547 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 778 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ASN A 778 " 0.023 2.00e-02 2.50e+03 pdb=" O ASN A 778 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 779 " -0.008 2.00e-02 2.50e+03 ... (remaining 1274 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 3 2.47 - 3.08: 5102 3.08 - 3.69: 10505 3.69 - 4.29: 14875 4.29 - 4.90: 24766 Nonbonded interactions: 55251 Sorted by model distance: nonbonded pdb=" F1 BEF A1301 " pdb="MG MG A1302 " model vdw 1.866 2.120 nonbonded pdb=" OD1 ASP A 775 " pdb="MG MG A1302 " model vdw 2.023 2.170 nonbonded pdb=" O THR A 456 " pdb="MG MG A1302 " model vdw 2.032 2.170 nonbonded pdb=" O ASP A 810 " pdb=" OD1 ASP A 811 " model vdw 2.568 3.040 nonbonded pdb=" CG ASP A 454 " pdb=" F3 BEF A1301 " model vdw 2.602 2.576 ... (remaining 55246 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.300 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 : 0.011 0.898 7485 Z= 1.053 Angle : 0.650 17.981 10146 Z= 0.304 Chirality : 0.041 0.132 1202 Planarity : 0.004 0.044 1277 Dihedral : 13.218 135.594 2832 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.10 % Allowed : 9.33 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.27), residues: 933 helix: 0.53 (0.25), residues: 457 sheet: 0.35 (0.58), residues: 85 loop : -1.17 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 59 TYR 0.008 0.001 TYR A 218 PHE 0.016 0.001 PHE A 833 TRP 0.009 0.001 TRP A 737 HIS 0.001 0.000 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 ( 7484) covalent geometry : angle 0.64986 / 0.30 (10146) hydrogen bonds : bond 0.20886 / 13.75 ( 348) hydrogen bonds : angle 6.99552 / 4.98 ( 1029) Misc. bond : bond 0.89803 / 56.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.213 Fit side-chains REVERT: A 78 ARG cc_start: 0.7670 (mmm160) cc_final: 0.7413 (mmm160) REVERT: A 84 GLN cc_start: 0.6557 (mt0) cc_final: 0.6147 (tp-100) REVERT: A 112 GLU cc_start: 0.7923 (tt0) cc_final: 0.7600 (pt0) REVERT: A 249 ARG cc_start: 0.7968 (ptm160) cc_final: 0.7242 (ptm-80) REVERT: A 255 ASP cc_start: 0.7366 (t70) cc_final: 0.6954 (t70) REVERT: A 610 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7292 (mp0) REVERT: A 613 LYS cc_start: 0.7453 (tppt) cc_final: 0.7200 (tppt) REVERT: A 1009 PHE cc_start: 0.8171 (m-80) cc_final: 0.7879 (m-80) outliers start: 9 outliers final: 4 residues processed: 128 average time/residue: 0.0778 time to fit residues: 13.6499 Evaluate side-chains 115 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 869 ASN A 967 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.181527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.104931 restraints weight = 8143.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.108260 restraints weight = 5940.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.110047 restraints weight = 4894.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.111567 restraints weight = 4368.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112726 restraints weight = 4022.141| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7485 Z= 0.224 Angle : 0.619 5.768 10146 Z= 0.331 Chirality : 0.046 0.153 1202 Planarity : 0.005 0.048 1277 Dihedral : 7.477 132.933 1062 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.31 % Allowed : 13.87 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.27), residues: 933 helix: 0.50 (0.24), residues: 478 sheet: 0.52 (0.58), residues: 77 loop : -1.27 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 892 TYR 0.009 0.001 TYR A 827 PHE 0.026 0.002 PHE A 836 TRP 0.011 0.001 TRP A 737 HIS 0.005 0.001 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.22 ( 7484) covalent geometry : angle 0.61853 / 0.33 (10146) hydrogen bonds : bond 0.06556 / 4.35 ( 348) hydrogen bonds : angle 5.02138 / 3.65 ( 1029) Misc. bond : bond 0.00277 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.274 Fit side-chains REVERT: A 84 GLN cc_start: 0.6576 (mt0) cc_final: 0.6103 (tp-100) REVERT: A 112 GLU cc_start: 0.8001 (tt0) cc_final: 0.7669 (pt0) REVERT: A 249 ARG cc_start: 0.7898 (ptm160) cc_final: 0.7193 (ptm-80) REVERT: A 255 ASP cc_start: 0.7504 (t70) cc_final: 0.7166 (t70) REVERT: A 610 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7321 (tp30) REVERT: A 611 MET cc_start: 0.8964 (mmp) cc_final: 0.8750 (mmp) REVERT: A 870 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8447 (mm) outliers start: 27 outliers final: 15 residues processed: 135 average time/residue: 0.0746 time to fit residues: 14.1870 Evaluate side-chains 121 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1002 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 61 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 967 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.181958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.104386 restraints weight = 8063.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.108175 restraints weight = 5593.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110725 restraints weight = 4518.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111974 restraints weight = 3980.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.112238 restraints weight = 3690.977| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7485 Z= 0.180 Angle : 0.566 5.700 10146 Z= 0.301 Chirality : 0.044 0.144 1202 Planarity : 0.004 0.042 1277 Dihedral : 7.192 127.881 1061 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.80 % Allowed : 16.20 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.27), residues: 933 helix: 0.66 (0.24), residues: 480 sheet: 0.35 (0.58), residues: 77 loop : -1.29 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 824 TYR 0.018 0.001 TYR A 218 PHE 0.021 0.002 PHE A 836 TRP 0.013 0.001 TRP A 737 HIS 0.002 0.001 HIS A 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 ( 7484) covalent geometry : angle 0.56602 / 0.30 (10146) hydrogen bonds : bond 0.05921 / 3.94 ( 348) hydrogen bonds : angle 4.69112 / 3.42 ( 1029) Misc. bond : bond 0.00202 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.172 Fit side-chains REVERT: A 84 GLN cc_start: 0.6561 (mt0) cc_final: 0.5979 (tp-100) REVERT: A 112 GLU cc_start: 0.7946 (tt0) cc_final: 0.7639 (pt0) REVERT: A 249 ARG cc_start: 0.7887 (ptm160) cc_final: 0.7206 (ptm-80) REVERT: A 255 ASP cc_start: 0.7505 (t70) cc_final: 0.7225 (t70) REVERT: A 870 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8523 (mm) REVERT: A 995 PHE cc_start: 0.7864 (t80) cc_final: 0.7509 (t80) REVERT: A 1029 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7597 (tt0) outliers start: 31 outliers final: 18 residues processed: 130 average time/residue: 0.0697 time to fit residues: 12.7772 Evaluate side-chains 128 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1029 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.184393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109992 restraints weight = 8115.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.114009 restraints weight = 5904.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.115211 restraints weight = 4563.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.117126 restraints weight = 4049.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117246 restraints weight = 3888.279| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7485 Z= 0.132 Angle : 0.528 5.790 10146 Z= 0.277 Chirality : 0.042 0.156 1202 Planarity : 0.004 0.041 1277 Dihedral : 6.991 125.573 1061 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.93 % Allowed : 17.06 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.27), residues: 933 helix: 0.88 (0.25), residues: 481 sheet: 0.36 (0.59), residues: 77 loop : -1.18 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 824 TYR 0.005 0.001 TYR A 503 PHE 0.018 0.001 PHE A 836 TRP 0.013 0.001 TRP A 737 HIS 0.002 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 7484) covalent geometry : angle 0.52784 / 0.28 (10146) hydrogen bonds : bond 0.05036 / 3.36 ( 348) hydrogen bonds : angle 4.44414 / 3.22 ( 1029) Misc. bond : bond 0.00127 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.173 Fit side-chains REVERT: A 84 GLN cc_start: 0.6566 (mt0) cc_final: 0.5902 (tp-100) REVERT: A 112 GLU cc_start: 0.7976 (tt0) cc_final: 0.7611 (pt0) REVERT: A 249 ARG cc_start: 0.7849 (ptm160) cc_final: 0.7157 (ptm-80) REVERT: A 255 ASP cc_start: 0.7458 (t70) cc_final: 0.7185 (t70) REVERT: A 505 THR cc_start: 0.8770 (m) cc_final: 0.8474 (p) REVERT: A 611 MET cc_start: 0.9048 (mmp) cc_final: 0.8797 (mmp) REVERT: A 870 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8525 (mm) REVERT: A 995 PHE cc_start: 0.7752 (t80) cc_final: 0.7411 (t80) REVERT: A 1009 PHE cc_start: 0.8409 (m-80) cc_final: 0.7903 (m-80) REVERT: A 1029 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7579 (tt0) outliers start: 32 outliers final: 24 residues processed: 134 average time/residue: 0.0649 time to fit residues: 12.5597 Evaluate side-chains 132 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1029 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 967 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.179496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.101595 restraints weight = 8175.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.105100 restraints weight = 5793.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.107468 restraints weight = 4726.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.108654 restraints weight = 4170.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109704 restraints weight = 3884.750| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 7485 Z= 0.224 Angle : 0.601 6.112 10146 Z= 0.321 Chirality : 0.046 0.165 1202 Planarity : 0.004 0.041 1277 Dihedral : 7.134 128.514 1061 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.40 % Allowed : 17.79 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.27), residues: 933 helix: 0.68 (0.24), residues: 478 sheet: 0.07 (0.60), residues: 77 loop : -1.24 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 824 TYR 0.018 0.001 TYR A 218 PHE 0.025 0.002 PHE A 836 TRP 0.013 0.001 TRP A 737 HIS 0.003 0.001 HIS A 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.22 ( 7484) covalent geometry : angle 0.60063 / 0.32 (10146) hydrogen bonds : bond 0.06130 / 4.08 ( 348) hydrogen bonds : angle 4.58274 / 3.35 ( 1029) Misc. bond : bond 0.00246 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 84 GLN cc_start: 0.6620 (mt0) cc_final: 0.5985 (tp-100) REVERT: A 112 GLU cc_start: 0.7984 (tt0) cc_final: 0.7690 (pt0) REVERT: A 182 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6328 (pp) REVERT: A 611 MET cc_start: 0.8911 (mmp) cc_final: 0.8705 (mmp) REVERT: A 870 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8687 (mm) REVERT: A 906 MET cc_start: 0.8524 (mtp) cc_final: 0.8288 (mtp) REVERT: A 995 PHE cc_start: 0.7991 (t80) cc_final: 0.7620 (t80) REVERT: A 1009 PHE cc_start: 0.8319 (m-80) cc_final: 0.7864 (m-80) REVERT: A 1029 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7825 (tt0) outliers start: 44 outliers final: 37 residues processed: 136 average time/residue: 0.0700 time to fit residues: 13.3490 Evaluate side-chains 144 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1029 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 41 optimal weight: 0.0020 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.0070 chunk 31 optimal weight: 0.0870 chunk 76 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 967 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.185438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.108504 restraints weight = 7952.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.112396 restraints weight = 5534.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115006 restraints weight = 4371.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116197 restraints weight = 3819.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.117056 restraints weight = 3546.639| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7485 Z= 0.110 Angle : 0.507 5.995 10146 Z= 0.267 Chirality : 0.041 0.151 1202 Planarity : 0.004 0.040 1277 Dihedral : 6.756 122.113 1061 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.42 % Allowed : 19.39 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.28), residues: 933 helix: 1.07 (0.25), residues: 480 sheet: 0.16 (0.59), residues: 77 loop : -1.10 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.021 0.001 TYR A 218 PHE 0.016 0.001 PHE A 833 TRP 0.015 0.001 TRP A 737 HIS 0.002 0.000 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 7484) covalent geometry : angle 0.50684 / 0.27 (10146) hydrogen bonds : bond 0.04447 / 2.99 ( 348) hydrogen bonds : angle 4.21271 / 3.06 ( 1029) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 84 GLN cc_start: 0.6482 (mt0) cc_final: 0.5882 (tp-100) REVERT: A 112 GLU cc_start: 0.7977 (tt0) cc_final: 0.7733 (pt0) REVERT: A 182 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6201 (pp) REVERT: A 221 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8741 (tt) REVERT: A 247 GLN cc_start: 0.8103 (mt0) cc_final: 0.7887 (mt0) REVERT: A 249 ARG cc_start: 0.7872 (ptm160) cc_final: 0.7286 (ptm-80) REVERT: A 505 THR cc_start: 0.8836 (m) cc_final: 0.8579 (p) REVERT: A 906 MET cc_start: 0.8353 (mtp) cc_final: 0.8110 (mtp) REVERT: A 995 PHE cc_start: 0.7876 (t80) cc_final: 0.7533 (t80) REVERT: A 1009 PHE cc_start: 0.8276 (m-80) cc_final: 0.7893 (m-80) REVERT: A 1029 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7094 (tp30) outliers start: 36 outliers final: 23 residues processed: 135 average time/residue: 0.0628 time to fit residues: 12.1865 Evaluate side-chains 131 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1041 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 14 optimal weight: 0.0870 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 16 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.185979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112776 restraints weight = 8008.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116074 restraints weight = 5969.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.117312 restraints weight = 4884.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117535 restraints weight = 4349.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.117900 restraints weight = 4432.487| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7485 Z= 0.125 Angle : 0.518 7.109 10146 Z= 0.270 Chirality : 0.042 0.168 1202 Planarity : 0.004 0.039 1277 Dihedral : 6.712 122.784 1060 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.17 % Allowed : 19.75 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 933 helix: 1.16 (0.25), residues: 480 sheet: 0.09 (0.58), residues: 77 loop : -1.17 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 608 TYR 0.023 0.001 TYR A 218 PHE 0.017 0.001 PHE A 836 TRP 0.014 0.001 TRP A 737 HIS 0.002 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 7484) covalent geometry : angle 0.51844 / 0.27 (10146) hydrogen bonds : bond 0.04583 / 3.07 ( 348) hydrogen bonds : angle 4.20853 / 3.04 ( 1029) Misc. bond : bond 0.00108 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7971 (tt0) cc_final: 0.7738 (pt0) REVERT: A 182 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6263 (pp) REVERT: A 221 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8723 (tt) REVERT: A 247 GLN cc_start: 0.8133 (mt0) cc_final: 0.7900 (mt0) REVERT: A 249 ARG cc_start: 0.7851 (ptm160) cc_final: 0.7257 (ptm-80) REVERT: A 481 ASP cc_start: 0.8942 (t70) cc_final: 0.8125 (p0) REVERT: A 505 THR cc_start: 0.8826 (m) cc_final: 0.8583 (p) REVERT: A 617 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: A 906 MET cc_start: 0.8426 (mtp) cc_final: 0.8205 (mtp) REVERT: A 995 PHE cc_start: 0.7922 (t80) cc_final: 0.7559 (t80) REVERT: A 1009 PHE cc_start: 0.8363 (m-80) cc_final: 0.7962 (m-80) REVERT: A 1029 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7458 (mm-30) outliers start: 34 outliers final: 27 residues processed: 128 average time/residue: 0.0638 time to fit residues: 11.7802 Evaluate side-chains 133 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1041 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 0.0270 chunk 38 optimal weight: 6.9990 chunk 5 optimal weight: 0.0370 chunk 42 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.185267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.111101 restraints weight = 8116.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.112510 restraints weight = 5561.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.114171 restraints weight = 4740.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.114874 restraints weight = 4056.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115319 restraints weight = 3995.610| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7485 Z= 0.118 Angle : 0.525 8.257 10146 Z= 0.271 Chirality : 0.042 0.178 1202 Planarity : 0.004 0.038 1277 Dihedral : 6.604 121.288 1060 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.42 % Allowed : 20.12 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.27), residues: 933 helix: 1.25 (0.25), residues: 479 sheet: 0.11 (0.57), residues: 77 loop : -1.18 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 543 TYR 0.025 0.001 TYR A 218 PHE 0.016 0.001 PHE A 833 TRP 0.014 0.001 TRP A 737 HIS 0.002 0.000 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7484) covalent geometry : angle 0.52455 / 0.27 (10146) hydrogen bonds : bond 0.04330 / 2.91 ( 348) hydrogen bonds : angle 4.11867 / 2.97 ( 1029) Misc. bond : bond 0.00082 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7736 (pt0) REVERT: A 182 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6185 (pp) REVERT: A 221 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8677 (tt) REVERT: A 247 GLN cc_start: 0.8060 (mt0) cc_final: 0.7829 (mt0) REVERT: A 249 ARG cc_start: 0.7890 (ptm160) cc_final: 0.7267 (ptm-80) REVERT: A 481 ASP cc_start: 0.8995 (t70) cc_final: 0.8202 (p0) REVERT: A 505 THR cc_start: 0.8755 (m) cc_final: 0.8545 (p) REVERT: A 617 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: A 906 MET cc_start: 0.8394 (mtp) cc_final: 0.8158 (mtp) REVERT: A 995 PHE cc_start: 0.7928 (t80) cc_final: 0.7536 (t80) REVERT: A 1009 PHE cc_start: 0.8386 (m-80) cc_final: 0.7920 (m-80) REVERT: A 1025 ILE cc_start: 0.8967 (tp) cc_final: 0.8756 (tp) REVERT: A 1029 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7410 (mm-30) outliers start: 36 outliers final: 30 residues processed: 132 average time/residue: 0.0591 time to fit residues: 11.2731 Evaluate side-chains 137 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1041 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 82 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 967 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.183610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.107920 restraints weight = 7977.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.109399 restraints weight = 6379.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110828 restraints weight = 4821.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.111835 restraints weight = 4298.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.112131 restraints weight = 4158.115| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7485 Z= 0.134 Angle : 0.539 8.261 10146 Z= 0.278 Chirality : 0.042 0.188 1202 Planarity : 0.004 0.037 1277 Dihedral : 6.632 122.282 1060 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.28 % Allowed : 19.26 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.27), residues: 933 helix: 1.24 (0.25), residues: 479 sheet: 0.09 (0.57), residues: 77 loop : -1.19 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 892 TYR 0.024 0.001 TYR A 218 PHE 0.018 0.001 PHE A 836 TRP 0.013 0.001 TRP A 737 HIS 0.003 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 7484) covalent geometry : angle 0.53876 / 0.28 (10146) hydrogen bonds : bond 0.04625 / 3.10 ( 348) hydrogen bonds : angle 4.15767 / 2.99 ( 1029) Misc. bond : bond 0.00110 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7753 (pt0) REVERT: A 182 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6086 (pp) REVERT: A 221 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8702 (tt) REVERT: A 247 GLN cc_start: 0.8136 (mt0) cc_final: 0.7900 (mt0) REVERT: A 249 ARG cc_start: 0.7877 (ptm160) cc_final: 0.7293 (ptm-80) REVERT: A 481 ASP cc_start: 0.8968 (t70) cc_final: 0.8210 (p0) REVERT: A 505 THR cc_start: 0.8811 (m) cc_final: 0.8605 (p) REVERT: A 617 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: A 901 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7808 (tt) REVERT: A 906 MET cc_start: 0.8444 (mtp) cc_final: 0.8231 (mtp) REVERT: A 995 PHE cc_start: 0.7937 (t80) cc_final: 0.7520 (t80) REVERT: A 1009 PHE cc_start: 0.8438 (m-80) cc_final: 0.7936 (m-80) REVERT: A 1029 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7472 (mm-30) outliers start: 43 outliers final: 33 residues processed: 135 average time/residue: 0.0585 time to fit residues: 11.5256 Evaluate side-chains 141 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1041 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 0.0670 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 chunk 72 optimal weight: 0.5980 chunk 82 optimal weight: 0.2980 chunk 52 optimal weight: 0.0000 chunk 65 optimal weight: 0.9990 overall best weight: 0.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 967 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.187936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.118191 restraints weight = 7947.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.118176 restraints weight = 5958.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.118494 restraints weight = 4706.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118546 restraints weight = 4522.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118878 restraints weight = 4336.561| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7485 Z= 0.107 Angle : 0.519 7.829 10146 Z= 0.270 Chirality : 0.041 0.176 1202 Planarity : 0.004 0.038 1277 Dihedral : 6.457 118.881 1060 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.56 % Allowed : 21.23 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.28), residues: 933 helix: 1.43 (0.25), residues: 479 sheet: 0.25 (0.57), residues: 77 loop : -1.09 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 543 TYR 0.025 0.001 TYR A 218 PHE 0.014 0.001 PHE A 833 TRP 0.016 0.001 TRP A 737 HIS 0.002 0.000 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 7484) covalent geometry : angle 0.51905 / 0.27 (10146) hydrogen bonds : bond 0.03772 / 2.55 ( 348) hydrogen bonds : angle 4.00632 / 2.88 ( 1029) Misc. bond : bond 0.00045 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7926 (tt0) cc_final: 0.7691 (pt0) REVERT: A 182 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6249 (pp) REVERT: A 221 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8699 (tt) REVERT: A 247 GLN cc_start: 0.7935 (mt0) cc_final: 0.7715 (mt0) REVERT: A 249 ARG cc_start: 0.7904 (ptm160) cc_final: 0.7362 (ptm-80) REVERT: A 564 MET cc_start: 0.8059 (tmm) cc_final: 0.7789 (tmm) REVERT: A 611 MET cc_start: 0.8756 (mmp) cc_final: 0.8456 (mmp) REVERT: A 617 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: A 906 MET cc_start: 0.8295 (mtp) cc_final: 0.8084 (mtp) REVERT: A 1009 PHE cc_start: 0.8356 (m-80) cc_final: 0.7923 (m-80) REVERT: A 1029 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7516 (tt0) outliers start: 29 outliers final: 23 residues processed: 131 average time/residue: 0.0680 time to fit residues: 12.6965 Evaluate side-chains 130 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 967 ASN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1041 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 41 optimal weight: 0.0870 chunk 58 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 967 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.187883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112814 restraints weight = 7947.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116290 restraints weight = 5637.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118665 restraints weight = 4604.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.119540 restraints weight = 4065.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120870 restraints weight = 3816.806| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 7485 Z= 0.170 Angle : 0.912 59.193 10146 Z= 0.545 Chirality : 0.046 0.612 1202 Planarity : 0.005 0.100 1277 Dihedral : 6.443 118.921 1059 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.44 % Allowed : 21.60 % Favored : 74.97 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.28), residues: 933 helix: 1.42 (0.25), residues: 479 sheet: 0.26 (0.57), residues: 77 loop : -1.09 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 196 TYR 0.024 0.001 TYR A 218 PHE 0.032 0.001 PHE A 995 TRP 0.014 0.001 TRP A 737 HIS 0.002 0.000 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 ( 7484) covalent geometry : angle 0.91170 / 0.54 (10146) hydrogen bonds : bond 0.03807 / 2.57 ( 348) hydrogen bonds : angle 4.01569 / 2.88 ( 1029) Misc. bond : bond 0.00064 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1381.55 seconds wall clock time: 24 minutes 26.09 seconds (1466.09 seconds total)