Starting phenix.real_space_refine on Fri Sep 11 05:23:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ln7_0926/09_2026/6ln7_0926.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ln7_0926/09_2026/6ln7_0926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ln7_0926/09_2026/6ln7_0926.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ln7_0926/09_2026/6ln7_0926.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ln7_0926/09_2026/6ln7_0926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ln7_0926/09_2026/6ln7_0926.map" model { file = "/net/cci-nas-00/data/ceres_data/6ln7_0926/09_2026/6ln7_0926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ln7_0926/09_2026/6ln7_0926.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 4988 2.51 5 N 1311 2.21 5 O 1478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7840 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7806 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 46, 'TRANS': 964} Chain breaks: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' MG': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.71, per 1000 atoms: 0.22 Number of scatterers: 7840 At special positions: 0 Unit cell: (103.335, 80.925, 139.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 57 16.00 P 3 15.00 Mg 1 11.99 O 1478 8.00 N 1311 7.00 C 4988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 430.4 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 53.7% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 removed outlier: 3.618A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 59 through 79 removed outlier: 3.897A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 88 through 118 removed outlier: 3.815A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 226 through 229 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.501A pdb=" N ILE A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 275 removed outlier: 3.541A pdb=" N ASN A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.586A pdb=" N PHE A 279 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN A 280 " --> pdb=" O GLY A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 276 through 280' Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 287 through 307 Processing helix chain 'A' and resid 310 through 328 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 439 through 452 removed outlier: 3.650A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 477 removed outlier: 3.569A pdb=" N VAL A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 475 " --> pdb=" O CYS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 522 Processing helix chain 'A' and resid 537 through 553 Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.656A pdb=" N TYR A 586 " --> pdb=" O ASN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 672 removed outlier: 3.806A pdb=" N CYS A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 removed outlier: 3.679A pdb=" N SER A 684 " --> pdb=" O PRO A 680 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'A' and resid 739 through 781 removed outlier: 4.004A pdb=" N VAL A 743 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 799 Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 806 through 809 Processing helix chain 'A' and resid 829 through 857 removed outlier: 3.648A pdb=" N ALA A 851 " --> pdb=" O THR A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 872 through 875 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.579A pdb=" N PHE A 890 " --> pdb=" O CYS A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.348A pdb=" N MET A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 928 Processing helix chain 'A' and resid 929 through 949 Processing helix chain 'A' and resid 951 through 957 removed outlier: 3.772A pdb=" N ILE A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 974 through 992 removed outlier: 3.797A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 992 " --> pdb=" O ARG A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1030 removed outlier: 3.621A pdb=" N LEU A1021 " --> pdb=" O PRO A1017 " (cutoff:3.500A) Proline residue: A1024 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 141 removed outlier: 4.321A pdb=" N LYS A 128 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A 150 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET A 220 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.748A pdb=" N LEU A 173 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG A 174 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.342A pdb=" N GLY A 716 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU A 734 " --> pdb=" O GLY A 716 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA A 718 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET A 699 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N MET A 719 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLY A 701 " --> pdb=" O MET A 719 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 350 removed outlier: 8.131A pdb=" N PHE A 675 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N MET A 622 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE A 652 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.615A pdb=" N THR A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL A 372 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 19.652A pdb=" N CYS A 524 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 17.375A pdb=" N PHE A 367 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 14.855A pdb=" N HIS A 526 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 10.400A pdb=" N LEU A 369 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG A 528 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ARG A 371 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 532 through 535 removed outlier: 5.774A pdb=" N LEU A 590 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY A 594 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 16.175A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 14.534A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL A 372 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.615A pdb=" N THR A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL A 372 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.534A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 16.175A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N PHE A 592 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR A 565 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER A 493 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU A 486 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER A 495 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR A 484 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR A 497 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 424 through 428 443 hydrogen bonds defined for protein. 1275 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: 1.58 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2578 1.35 - 1.48: 1791 1.48 - 1.61: 3522 1.61 - 1.73: 4 1.73 - 1.86: 90 Bond restraints: 7985 Sorted by residual: bond pdb=" C1' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.390 1.618 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ACP A2001 " pdb=" C2' ACP A2001 " ideal model delta sigma weight residual 1.527 1.307 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C4' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.428 1.301 0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 1.335 1.449 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C2' ACP A2001 " pdb=" O2' ACP A2001 " ideal model delta sigma weight residual 1.401 1.494 -0.093 2.00e-02 2.50e+03 2.16e+01 ... (remaining 7980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 10786 3.15 - 6.30: 49 6.30 - 9.45: 4 9.45 - 12.60: 4 12.60 - 15.75: 1 Bond angle restraints: 10844 Sorted by residual: angle pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O5' ACP A2001 " ideal model delta sigma weight residual 93.75 109.50 -15.75 3.00e+00 1.11e-01 2.76e+01 angle pdb=" C3B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O3A ACP A2001 " ideal model delta sigma weight residual 98.05 110.64 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N1 ACP A2001 " pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 119.32 108.35 10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O1B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O2B ACP A2001 " ideal model delta sigma weight residual 119.60 108.99 10.61 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O1A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O2A ACP A2001 " ideal model delta sigma weight residual 118.95 108.65 10.30 3.00e+00 1.11e-01 1.18e+01 ... (remaining 10839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.02: 4699 26.02 - 52.04: 121 52.04 - 78.06: 7 78.06 - 104.08: 2 104.08 - 130.10: 1 Dihedral angle restraints: 4830 sinusoidal: 1910 harmonic: 2920 Sorted by residual: dihedral pdb=" O1A ACP A2001 " pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" PB ACP A2001 " ideal model delta sinusoidal sigma weight residual -48.75 81.35 -130.10 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" CA VAL A 949 " pdb=" C VAL A 949 " pdb=" N GLU A 950 " pdb=" CA GLU A 950 " ideal model delta harmonic sigma weight residual -180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASP A 370 " pdb=" CB ASP A 370 " pdb=" CG ASP A 370 " pdb=" OD1 ASP A 370 " ideal model delta sinusoidal sigma weight residual -30.00 -87.58 57.58 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 4827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1184 0.078 - 0.155: 88 0.155 - 0.233: 0 0.233 - 0.310: 0 0.310 - 0.388: 1 Chirality restraints: 1273 Sorted by residual: chirality pdb=" C2' ACP A2001 " pdb=" C1' ACP A2001 " pdb=" C3' ACP A2001 " pdb=" O2' ACP A2001 " both_signs ideal model delta sigma weight residual False -2.75 -2.36 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA ILE A 623 " pdb=" N ILE A 623 " pdb=" C ILE A 623 " pdb=" CB ILE A 623 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CG LEU A 806 " pdb=" CB LEU A 806 " pdb=" CD1 LEU A 806 " pdb=" CD2 LEU A 806 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1270 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1016 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A1017 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A1017 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1017 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 975 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 194 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 195 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 195 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 195 " 0.019 5.00e-02 4.00e+02 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 119 2.66 - 3.22: 7357 3.22 - 3.78: 11988 3.78 - 4.34: 17673 4.34 - 4.90: 28382 Nonbonded interactions: 65519 Sorted by model distance: nonbonded pdb=" OD1 ASP A 351 " pdb="MG MG A2002 " model vdw 2.101 2.170 nonbonded pdb=" OE2 GLU A 309 " pdb=" OD1 ASN A 795 " model vdw 2.114 3.040 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.134 2.170 nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.138 2.170 nonbonded pdb=" O ILE A 307 " pdb=" OE1 GLU A 309 " model vdw 2.150 3.040 ... (remaining 65514 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.500 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 7985 Z= 0.261 Angle : 0.647 15.750 10844 Z= 0.341 Chirality : 0.042 0.388 1273 Planarity : 0.004 0.041 1377 Dihedral : 11.725 130.104 2938 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.20), residues: 1007 helix: -3.29 (0.13), residues: 501 sheet: -1.13 (0.46), residues: 113 loop : -1.80 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 666 TYR 0.009 0.001 TYR A 842 PHE 0.010 0.001 PHE A 367 TRP 0.009 0.001 TRP A 793 HIS 0.005 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.26 ( 7985) covalent geometry : angle 0.64659 / 0.34 (10844) hydrogen bonds : bond 0.24755 / 16.43 ( 419) hydrogen bonds : angle 8.90669 / 6.32 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.298 Fit side-chains REVERT: A 1 MET cc_start: 0.7214 (tpp) cc_final: 0.6660 (tpp) REVERT: A 33 LYS cc_start: 0.8417 (tmtt) cc_final: 0.7918 (ttmm) REVERT: A 254 ASP cc_start: 0.7702 (m-30) cc_final: 0.7412 (m-30) REVERT: A 365 ARG cc_start: 0.7824 (mtt90) cc_final: 0.7414 (mtt180) REVERT: A 381 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8133 (mt-10) REVERT: A 494 MET cc_start: 0.8920 (ttt) cc_final: 0.8596 (ttm) REVERT: A 732 MET cc_start: 0.8594 (ttt) cc_final: 0.8393 (ttp) REVERT: A 824 LYS cc_start: 0.8486 (mttm) cc_final: 0.8238 (mptt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.6504 time to fit residues: 115.0667 Evaluate side-chains 113 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 190 HIS A 278 HIS A 469 ASN A 582 ASN A 868 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.129072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.098268 restraints weight = 8804.874| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.74 r_work: 0.2949 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7985 Z= 0.120 Angle : 0.538 6.331 10844 Z= 0.279 Chirality : 0.041 0.130 1273 Planarity : 0.005 0.047 1377 Dihedral : 6.466 144.081 1075 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.50 % Allowed : 12.96 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.24), residues: 1007 helix: -0.24 (0.21), residues: 508 sheet: -0.80 (0.44), residues: 116 loop : -1.02 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 821 TYR 0.012 0.002 TYR A 295 PHE 0.020 0.001 PHE A 367 TRP 0.012 0.001 TRP A 854 HIS 0.003 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7985) covalent geometry : angle 0.53762 / 0.28 (10844) hydrogen bonds : bond 0.04755 / 3.19 ( 419) hydrogen bonds : angle 4.61899 / 3.18 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.440 Fit side-chains REVERT: A 33 LYS cc_start: 0.8605 (tmtt) cc_final: 0.7931 (ttmm) REVERT: A 51 GLU cc_start: 0.7318 (tp30) cc_final: 0.6957 (tm-30) REVERT: A 135 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8386 (ttmm) REVERT: A 254 ASP cc_start: 0.7818 (m-30) cc_final: 0.7547 (m-30) REVERT: A 258 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7422 (mm-30) REVERT: A 324 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7897 (ttp-110) REVERT: A 365 ARG cc_start: 0.8538 (mtt90) cc_final: 0.8240 (mmm-85) REVERT: A 452 MET cc_start: 0.8564 (ptm) cc_final: 0.8337 (ptp) REVERT: A 466 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8096 (mp0) REVERT: A 494 MET cc_start: 0.9216 (ttt) cc_final: 0.8916 (ttm) REVERT: A 754 ASN cc_start: 0.9116 (m-40) cc_final: 0.8886 (m110) outliers start: 13 outliers final: 5 residues processed: 129 average time/residue: 0.5664 time to fit residues: 77.0260 Evaluate side-chains 120 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN A 643 GLN A 868 GLN ** A 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.125852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.095074 restraints weight = 8751.483| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.80 r_work: 0.2813 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7985 Z= 0.167 Angle : 0.572 6.528 10844 Z= 0.291 Chirality : 0.044 0.171 1273 Planarity : 0.005 0.057 1377 Dihedral : 6.839 155.262 1075 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.55 % Allowed : 14.24 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.26), residues: 1007 helix: 0.68 (0.23), residues: 509 sheet: -0.79 (0.45), residues: 122 loop : -0.86 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 821 TYR 0.015 0.002 TYR A 842 PHE 0.019 0.001 PHE A 367 TRP 0.013 0.001 TRP A 854 HIS 0.005 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 7985) covalent geometry : angle 0.57155 / 0.29 (10844) hydrogen bonds : bond 0.04805 / 3.21 ( 419) hydrogen bonds : angle 4.46939 / 3.07 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.221 Fit side-chains REVERT: A 11 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7335 (mt-10) REVERT: A 33 LYS cc_start: 0.8527 (tmtt) cc_final: 0.7808 (ttmm) REVERT: A 51 GLU cc_start: 0.7327 (tp30) cc_final: 0.6956 (tm-30) REVERT: A 59 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6727 (t70) REVERT: A 135 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8385 (ttmm) REVERT: A 203 ASP cc_start: 0.8343 (m-30) cc_final: 0.8115 (m-30) REVERT: A 246 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6394 (ptm160) REVERT: A 254 ASP cc_start: 0.7908 (m-30) cc_final: 0.7596 (m-30) REVERT: A 324 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7890 (ttp-110) REVERT: A 365 ARG cc_start: 0.8517 (mtt90) cc_final: 0.8158 (mmm-85) REVERT: A 452 MET cc_start: 0.8568 (ptm) cc_final: 0.8328 (ptp) REVERT: A 466 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8115 (mt-10) REVERT: A 494 MET cc_start: 0.9083 (ttt) cc_final: 0.8808 (ttm) REVERT: A 650 LYS cc_start: 0.8700 (mttt) cc_final: 0.8323 (mttp) REVERT: A 881 ASP cc_start: 0.8158 (m-30) cc_final: 0.7910 (m-30) outliers start: 22 outliers final: 7 residues processed: 134 average time/residue: 0.5318 time to fit residues: 75.2609 Evaluate side-chains 124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 1023 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 GLN A 913 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.103359 restraints weight = 8699.760| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.54 r_work: 0.2819 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7985 Z= 0.162 Angle : 0.560 6.381 10844 Z= 0.285 Chirality : 0.043 0.169 1273 Planarity : 0.005 0.055 1377 Dihedral : 6.966 159.086 1075 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.66 % Allowed : 15.97 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.26), residues: 1007 helix: 1.00 (0.23), residues: 511 sheet: -0.64 (0.47), residues: 116 loop : -0.77 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 572 TYR 0.016 0.002 TYR A 842 PHE 0.019 0.001 PHE A 367 TRP 0.013 0.001 TRP A 854 HIS 0.005 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 7985) covalent geometry : angle 0.56007 / 0.29 (10844) hydrogen bonds : bond 0.04538 / 3.03 ( 419) hydrogen bonds : angle 4.37874 / 3.00 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.274 Fit side-chains REVERT: A 11 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: A 33 LYS cc_start: 0.8554 (tmtt) cc_final: 0.7803 (ttmm) REVERT: A 59 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6810 (t70) REVERT: A 117 GLU cc_start: 0.8241 (tp30) cc_final: 0.8007 (tp30) REVERT: A 135 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8418 (ttmm) REVERT: A 172 THR cc_start: 0.8794 (t) cc_final: 0.8514 (p) REVERT: A 203 ASP cc_start: 0.8178 (m-30) cc_final: 0.7976 (m-30) REVERT: A 246 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6639 (ptm160) REVERT: A 254 ASP cc_start: 0.7914 (m-30) cc_final: 0.7673 (m-30) REVERT: A 324 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7853 (ttp-110) REVERT: A 365 ARG cc_start: 0.8534 (mtt90) cc_final: 0.8205 (mmm-85) REVERT: A 466 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8122 (mt-10) REVERT: A 494 MET cc_start: 0.9109 (ttt) cc_final: 0.8748 (ttm) REVERT: A 508 MET cc_start: 0.5743 (mpp) cc_final: 0.4006 (tpt) REVERT: A 585 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8354 (mtmt) REVERT: A 650 LYS cc_start: 0.8700 (mttt) cc_final: 0.8318 (mttp) REVERT: A 881 ASP cc_start: 0.8175 (m-30) cc_final: 0.7925 (m-30) outliers start: 23 outliers final: 12 residues processed: 130 average time/residue: 0.5833 time to fit residues: 79.8036 Evaluate side-chains 137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1023 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 19 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 0.0570 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.128093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.097876 restraints weight = 8764.310| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.77 r_work: 0.2810 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7985 Z= 0.125 Angle : 0.527 6.352 10844 Z= 0.269 Chirality : 0.042 0.162 1273 Planarity : 0.004 0.045 1377 Dihedral : 6.880 159.758 1075 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.43 % Allowed : 17.13 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 1007 helix: 1.31 (0.23), residues: 510 sheet: -0.52 (0.47), residues: 116 loop : -0.61 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 572 TYR 0.013 0.002 TYR A 842 PHE 0.018 0.001 PHE A 367 TRP 0.013 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 7985) covalent geometry : angle 0.52687 / 0.27 (10844) hydrogen bonds : bond 0.04005 / 2.69 ( 419) hydrogen bonds : angle 4.20347 / 2.87 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.303 Fit side-chains REVERT: A 11 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: A 33 LYS cc_start: 0.8563 (tmtt) cc_final: 0.7696 (tppp) REVERT: A 59 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6866 (t70) REVERT: A 135 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8369 (ttmm) REVERT: A 172 THR cc_start: 0.8828 (t) cc_final: 0.8550 (p) REVERT: A 246 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6775 (ptm160) REVERT: A 254 ASP cc_start: 0.8002 (m-30) cc_final: 0.7794 (m-30) REVERT: A 324 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7885 (ttp-110) REVERT: A 365 ARG cc_start: 0.8621 (mtt90) cc_final: 0.8299 (mmm-85) REVERT: A 466 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8141 (mt-10) REVERT: A 494 MET cc_start: 0.9113 (ttt) cc_final: 0.8804 (ttm) REVERT: A 508 MET cc_start: 0.5752 (mpp) cc_final: 0.3939 (tpt) REVERT: A 650 LYS cc_start: 0.8740 (mttt) cc_final: 0.8367 (mttp) REVERT: A 754 ASN cc_start: 0.9014 (m-40) cc_final: 0.8746 (m110) REVERT: A 876 LYS cc_start: 0.6682 (mtmm) cc_final: 0.5852 (mtmm) REVERT: A 881 ASP cc_start: 0.8248 (m-30) cc_final: 0.7984 (m-30) outliers start: 21 outliers final: 9 residues processed: 137 average time/residue: 0.5674 time to fit residues: 82.0061 Evaluate side-chains 131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 1023 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 0.0070 chunk 43 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 86 optimal weight: 0.0980 chunk 84 optimal weight: 0.7980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 GLN A 643 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.131127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.101344 restraints weight = 8748.669| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.76 r_work: 0.2882 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7985 Z= 0.094 Angle : 0.491 7.272 10844 Z= 0.249 Chirality : 0.040 0.147 1273 Planarity : 0.004 0.045 1377 Dihedral : 6.601 155.088 1075 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.74 % Allowed : 18.06 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.27), residues: 1007 helix: 1.65 (0.24), residues: 509 sheet: -0.49 (0.47), residues: 116 loop : -0.39 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 572 TYR 0.011 0.001 TYR A 842 PHE 0.016 0.001 PHE A 367 TRP 0.013 0.001 TRP A 854 HIS 0.002 0.000 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 ( 7985) covalent geometry : angle 0.49085 / 0.25 (10844) hydrogen bonds : bond 0.03403 / 2.30 ( 419) hydrogen bonds : angle 3.99324 / 2.73 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: A 33 LYS cc_start: 0.8644 (tmtt) cc_final: 0.7762 (tppp) REVERT: A 59 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6876 (t70) REVERT: A 135 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8422 (ttmm) REVERT: A 172 THR cc_start: 0.8868 (t) cc_final: 0.8583 (p) REVERT: A 246 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6700 (ptm160) REVERT: A 254 ASP cc_start: 0.7963 (m-30) cc_final: 0.7697 (m-30) REVERT: A 258 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7335 (mm-30) REVERT: A 324 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7878 (ttp-110) REVERT: A 365 ARG cc_start: 0.8622 (mtt90) cc_final: 0.8275 (mmm-85) REVERT: A 452 MET cc_start: 0.8557 (ptm) cc_final: 0.8282 (ptp) REVERT: A 466 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8128 (mt-10) REVERT: A 473 SER cc_start: 0.8531 (m) cc_final: 0.8246 (m) REVERT: A 494 MET cc_start: 0.9064 (ttt) cc_final: 0.8834 (ttm) REVERT: A 599 LEU cc_start: 0.8476 (pt) cc_final: 0.8123 (mp) REVERT: A 650 LYS cc_start: 0.8778 (mttt) cc_final: 0.8426 (mttp) REVERT: A 876 LYS cc_start: 0.6717 (mtmm) cc_final: 0.6267 (mtmm) REVERT: A 881 ASP cc_start: 0.8135 (m-30) cc_final: 0.7884 (m-30) outliers start: 15 outliers final: 3 residues processed: 132 average time/residue: 0.5669 time to fit residues: 78.9440 Evaluate side-chains 126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 902 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 5 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 GLN A 643 GLN A 754 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.127916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.097864 restraints weight = 8791.769| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.76 r_work: 0.2819 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7985 Z= 0.139 Angle : 0.544 8.684 10844 Z= 0.273 Chirality : 0.042 0.173 1273 Planarity : 0.004 0.047 1377 Dihedral : 6.875 160.103 1075 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.43 % Allowed : 18.29 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1007 helix: 1.57 (0.24), residues: 511 sheet: -0.42 (0.46), residues: 119 loop : -0.41 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 572 TYR 0.016 0.002 TYR A 842 PHE 0.021 0.001 PHE A 367 TRP 0.013 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 7985) covalent geometry : angle 0.54359 / 0.27 (10844) hydrogen bonds : bond 0.04058 / 2.71 ( 419) hydrogen bonds : angle 4.16936 / 2.85 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.293 Fit side-chains REVERT: A 11 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: A 33 LYS cc_start: 0.8675 (tmtt) cc_final: 0.7772 (tppp) REVERT: A 59 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6868 (t70) REVERT: A 135 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8375 (ttmm) REVERT: A 172 THR cc_start: 0.8836 (t) cc_final: 0.8567 (p) REVERT: A 208 LEU cc_start: 0.9008 (mt) cc_final: 0.8720 (mt) REVERT: A 246 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6757 (ptm160) REVERT: A 254 ASP cc_start: 0.8021 (m-30) cc_final: 0.7797 (m-30) REVERT: A 324 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7915 (ttp-110) REVERT: A 334 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8173 (mtp-110) REVERT: A 365 ARG cc_start: 0.8602 (mtt90) cc_final: 0.8279 (mmm-85) REVERT: A 465 ILE cc_start: 0.8706 (mt) cc_final: 0.8461 (mp) REVERT: A 466 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8065 (mt-10) REVERT: A 473 SER cc_start: 0.8491 (m) cc_final: 0.8233 (m) REVERT: A 494 MET cc_start: 0.9108 (ttt) cc_final: 0.8855 (ttm) REVERT: A 576 HIS cc_start: 0.7346 (m170) cc_final: 0.7065 (m-70) REVERT: A 599 LEU cc_start: 0.8497 (pt) cc_final: 0.8120 (mp) REVERT: A 650 LYS cc_start: 0.8764 (mttt) cc_final: 0.8401 (mttp) REVERT: A 876 LYS cc_start: 0.6686 (mtmm) cc_final: 0.6271 (mtmm) REVERT: A 881 ASP cc_start: 0.8349 (m-30) cc_final: 0.8079 (m-30) outliers start: 21 outliers final: 8 residues processed: 132 average time/residue: 0.5842 time to fit residues: 81.4939 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.128320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.098331 restraints weight = 8862.739| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.75 r_work: 0.2833 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7985 Z= 0.116 Angle : 0.521 9.870 10844 Z= 0.262 Chirality : 0.041 0.170 1273 Planarity : 0.004 0.044 1377 Dihedral : 6.800 159.724 1075 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.08 % Allowed : 18.98 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 1007 helix: 1.59 (0.23), residues: 513 sheet: -0.34 (0.47), residues: 119 loop : -0.30 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 572 TYR 0.013 0.001 TYR A 842 PHE 0.018 0.001 PHE A 367 TRP 0.013 0.001 TRP A 854 HIS 0.003 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7985) covalent geometry : angle 0.52141 / 0.26 (10844) hydrogen bonds : bond 0.03740 / 2.52 ( 419) hydrogen bonds : angle 4.09694 / 2.80 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.312 Fit side-chains REVERT: A 11 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: A 33 LYS cc_start: 0.8679 (tmtt) cc_final: 0.7775 (tppp) REVERT: A 59 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6866 (t70) REVERT: A 135 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8370 (ttmm) REVERT: A 172 THR cc_start: 0.8826 (t) cc_final: 0.8546 (p) REVERT: A 208 LEU cc_start: 0.8953 (mt) cc_final: 0.8625 (mt) REVERT: A 246 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6769 (ptm160) REVERT: A 254 ASP cc_start: 0.8111 (m-30) cc_final: 0.7866 (m-30) REVERT: A 324 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7910 (ttp-110) REVERT: A 334 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8181 (mtp-110) REVERT: A 365 ARG cc_start: 0.8582 (mtt90) cc_final: 0.8304 (mmm-85) REVERT: A 465 ILE cc_start: 0.8703 (mt) cc_final: 0.8471 (mp) REVERT: A 466 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8101 (mt-10) REVERT: A 473 SER cc_start: 0.8498 (m) cc_final: 0.8228 (m) REVERT: A 491 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8403 (ttp-170) REVERT: A 494 MET cc_start: 0.9090 (ttt) cc_final: 0.8843 (ttm) REVERT: A 576 HIS cc_start: 0.7410 (m170) cc_final: 0.7127 (m-70) REVERT: A 599 LEU cc_start: 0.8519 (pt) cc_final: 0.8109 (mp) REVERT: A 650 LYS cc_start: 0.8769 (mttt) cc_final: 0.8403 (mttp) REVERT: A 876 LYS cc_start: 0.6667 (mtmm) cc_final: 0.6275 (mtmm) REVERT: A 881 ASP cc_start: 0.8351 (m-30) cc_final: 0.8078 (m-30) outliers start: 18 outliers final: 9 residues processed: 127 average time/residue: 0.5698 time to fit residues: 76.4434 Evaluate side-chains 130 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 902 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 38 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 88 optimal weight: 0.0770 chunk 87 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 ASN A 643 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.139325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.112216 restraints weight = 8583.716| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.56 r_work: 0.2894 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7985 Z= 0.096 Angle : 0.505 10.572 10844 Z= 0.253 Chirality : 0.041 0.169 1273 Planarity : 0.004 0.044 1377 Dihedral : 6.579 155.666 1075 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.20 % Allowed : 18.75 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.27), residues: 1007 helix: 1.76 (0.24), residues: 512 sheet: -0.29 (0.48), residues: 116 loop : -0.21 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 572 TYR 0.012 0.001 TYR A 842 PHE 0.018 0.001 PHE A 367 TRP 0.013 0.001 TRP A 854 HIS 0.002 0.000 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 7985) covalent geometry : angle 0.50480 / 0.25 (10844) hydrogen bonds : bond 0.03335 / 2.25 ( 419) hydrogen bonds : angle 3.97896 / 2.72 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.192 Fit side-chains REVERT: A 11 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: A 33 LYS cc_start: 0.8685 (tmtt) cc_final: 0.7780 (tppp) REVERT: A 59 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6801 (t70) REVERT: A 135 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8349 (ttmm) REVERT: A 172 THR cc_start: 0.8838 (t) cc_final: 0.8540 (p) REVERT: A 174 ARG cc_start: 0.8544 (mmm160) cc_final: 0.8249 (mtp85) REVERT: A 208 LEU cc_start: 0.8796 (mt) cc_final: 0.8516 (mt) REVERT: A 246 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6703 (ptm160) REVERT: A 254 ASP cc_start: 0.8012 (m-30) cc_final: 0.7753 (m-30) REVERT: A 324 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7837 (ttp-110) REVERT: A 334 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8157 (mtp-110) REVERT: A 365 ARG cc_start: 0.8523 (mtt90) cc_final: 0.8290 (mmm-85) REVERT: A 465 ILE cc_start: 0.8719 (mt) cc_final: 0.8495 (mp) REVERT: A 466 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8046 (mt-10) REVERT: A 473 SER cc_start: 0.8481 (m) cc_final: 0.8209 (m) REVERT: A 494 MET cc_start: 0.9036 (ttt) cc_final: 0.8790 (ttm) REVERT: A 576 HIS cc_start: 0.7449 (m170) cc_final: 0.7191 (m-70) REVERT: A 599 LEU cc_start: 0.8459 (pt) cc_final: 0.8101 (mp) REVERT: A 650 LYS cc_start: 0.8767 (mttt) cc_final: 0.8400 (mttp) REVERT: A 876 LYS cc_start: 0.6683 (mtmm) cc_final: 0.6298 (mtmm) REVERT: A 881 ASP cc_start: 0.8212 (m-30) cc_final: 0.7965 (m-30) REVERT: A 968 MET cc_start: 0.8620 (tpt) cc_final: 0.8363 (tpp) outliers start: 19 outliers final: 9 residues processed: 134 average time/residue: 0.5667 time to fit residues: 80.1938 Evaluate side-chains 131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 65 optimal weight: 0.0670 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 ASN A 453 ASN A 643 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.139834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112612 restraints weight = 8506.978| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.56 r_work: 0.2900 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7985 Z= 0.098 Angle : 0.513 12.450 10844 Z= 0.254 Chirality : 0.040 0.170 1273 Planarity : 0.004 0.042 1377 Dihedral : 6.540 154.649 1075 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.74 % Allowed : 19.56 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.27), residues: 1007 helix: 1.83 (0.24), residues: 512 sheet: -0.20 (0.48), residues: 119 loop : -0.13 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 572 TYR 0.012 0.001 TYR A 842 PHE 0.017 0.001 PHE A 367 TRP 0.013 0.001 TRP A 854 HIS 0.002 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 7985) covalent geometry : angle 0.51292 / 0.25 (10844) hydrogen bonds : bond 0.03329 / 2.24 ( 419) hydrogen bonds : angle 3.96276 / 2.71 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.297 Fit side-chains REVERT: A 33 LYS cc_start: 0.8718 (tmtt) cc_final: 0.7820 (tppp) REVERT: A 59 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6797 (t70) REVERT: A 172 THR cc_start: 0.8846 (t) cc_final: 0.8556 (p) REVERT: A 174 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8263 (mtp85) REVERT: A 208 LEU cc_start: 0.8777 (mt) cc_final: 0.8551 (mt) REVERT: A 246 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6636 (ptm160) REVERT: A 254 ASP cc_start: 0.8036 (m-30) cc_final: 0.7769 (m-30) REVERT: A 324 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7826 (ttp-110) REVERT: A 334 ARG cc_start: 0.8412 (mtp85) cc_final: 0.8140 (mtp-110) REVERT: A 365 ARG cc_start: 0.8532 (mtt90) cc_final: 0.8324 (mmm-85) REVERT: A 465 ILE cc_start: 0.8743 (mt) cc_final: 0.8532 (mp) REVERT: A 466 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8082 (mt-10) REVERT: A 473 SER cc_start: 0.8521 (m) cc_final: 0.8268 (m) REVERT: A 491 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8401 (ttp-170) REVERT: A 576 HIS cc_start: 0.7392 (m170) cc_final: 0.7144 (m-70) REVERT: A 599 LEU cc_start: 0.8442 (pt) cc_final: 0.8169 (mp) REVERT: A 650 LYS cc_start: 0.8793 (mttt) cc_final: 0.8460 (mttp) REVERT: A 876 LYS cc_start: 0.6694 (mtmm) cc_final: 0.6313 (mtmm) REVERT: A 881 ASP cc_start: 0.8165 (m-30) cc_final: 0.7927 (m-30) REVERT: A 968 MET cc_start: 0.8714 (tpt) cc_final: 0.8491 (tpp) outliers start: 15 outliers final: 9 residues processed: 134 average time/residue: 0.5487 time to fit residues: 77.9109 Evaluate side-chains 135 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 945 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 44 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 0.0870 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 GLN A 428 ASN A 453 ASN A 643 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.127101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.096451 restraints weight = 8734.049| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.81 r_work: 0.2808 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7985 Z= 0.139 Angle : 0.560 12.737 10844 Z= 0.277 Chirality : 0.043 0.173 1273 Planarity : 0.004 0.045 1377 Dihedral : 6.846 160.437 1075 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.85 % Allowed : 19.79 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.27), residues: 1007 helix: 1.69 (0.23), residues: 514 sheet: -0.28 (0.48), residues: 119 loop : -0.27 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 572 TYR 0.015 0.002 TYR A 842 PHE 0.019 0.001 PHE A 367 TRP 0.013 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 7985) covalent geometry : angle 0.55989 / 0.28 (10844) hydrogen bonds : bond 0.03978 / 2.66 ( 419) hydrogen bonds : angle 4.12836 / 2.82 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2898.40 seconds wall clock time: 50 minutes 2.18 seconds (3002.18 seconds total)