Starting phenix.real_space_refine on Fri Jul 3 00:08:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e1z_30947/07_2026/7e1z_30947_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e1z_30947/07_2026/7e1z_30947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e1z_30947/07_2026/7e1z_30947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e1z_30947/07_2026/7e1z_30947.map" model { file = "/net/cci-nas-00/data/ceres_data/7e1z_30947/07_2026/7e1z_30947_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e1z_30947/07_2026/7e1z_30947_neut.cif" } resolution = 3.2 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= 0.005 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 P 1 5.49 5 Mg 1 5.21 5 S 57 5.16 5 Na 4 4.78 5 C 6817 2.51 5 N 1714 2.21 5 O 1956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 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: 10550 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7575 Classifications: {'peptide': 976} Link IDs: {'PTRANS': 43, 'TRANS': 932} Chain breaks: 1 Chain: "B" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2404 Classifications: {'peptide': 294} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 273} Chain: "C" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 195 Ad-hoc single atom residues: {' NA': 4} Unusual residues: {' MG': 1, 'PC1': 1, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 4 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 1.95, per 1000 atoms: 0.18 Number of scatterers: 10550 At special positions: 0 Unit cell: (90.221, 96.743, 182.616, 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) S 57 16.00 P 1 15.00 Mg 1 11.99 Na 4 11.00 O 1956 8.00 N 1714 7.00 C 6817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 249 " distance=2.18 Simple disulfide: pdb=" SG CYS A 518 " - pdb=" SG CYS A 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=1.99 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 402 " - " ASN B 265 " " NAG D 1 " - " ASN B 158 " Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 229.1 milliseconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 13 sheets defined 44.2% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.787A pdb=" N GLN A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.807A pdb=" N ALA A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 159 removed outlier: 3.559A pdb=" N LEU A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 261 through 265 removed outlier: 4.007A pdb=" N ARG A 264 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 265 " --> pdb=" O GLY A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 265' Processing helix chain 'A' and resid 284 through 311 removed outlier: 3.748A pdb=" N ILE A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.990A pdb=" N THR A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.690A pdb=" N GLY A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 425 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.731A pdb=" N LYS A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 510 through 515 Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.607A pdb=" N ALA A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 604 " --> pdb=" O PRO A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.707A pdb=" N GLN A 654 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.506A pdb=" N LEU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS A 683 " --> pdb=" O ASP A 679 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 697 Processing helix chain 'A' and resid 698 through 707 removed outlier: 3.580A pdb=" N GLY A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 removed outlier: 3.824A pdb=" N LYS A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 745 removed outlier: 3.647A pdb=" N ALA A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.745A pdb=" N VAL A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP A 770 " --> pdb=" O ARG A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 796 Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 803 through 815 Processing helix chain 'A' and resid 820 through 825 removed outlier: 3.587A pdb=" N TYR A 824 " --> pdb=" O SER A 821 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 825 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.692A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 877 removed outlier: 3.998A pdb=" N ILE A 860 " --> pdb=" O GLN A 856 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 868 " --> pdb=" O GLY A 864 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 907 through 937 removed outlier: 3.777A pdb=" N ARG A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 947 Processing helix chain 'A' and resid 951 through 970 removed outlier: 3.758A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 removed outlier: 3.826A pdb=" N TRP A 988 " --> pdb=" O PRO A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1011 Processing helix chain 'A' and resid 1015 through 1022 removed outlier: 3.551A pdb=" N TYR A1022 " --> pdb=" O GLU A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 29 through 58 removed outlier: 3.518A pdb=" N PHE B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.595A pdb=" N GLN B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.636A pdb=" N TRP B 155 " --> pdb=" O LYS B 152 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 157 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.942A pdb=" N GLY B 172 " --> pdb=" O TYR B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 46 removed outlier: 3.690A pdb=" N GLY C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 193 removed outlier: 6.885A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 203 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 212 through 214 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.214A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR A 372 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR A 715 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N CYS A 374 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 387 through 388 removed outlier: 7.340A pdb=" N PHE A 555 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU A 588 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 553 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER A 590 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG A 551 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 509 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 432 through 433 removed outlier: 3.652A pdb=" N VAL A 432 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 479 removed outlier: 3.879A pdb=" N VAL A 478 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 521 through 522 Processing sheet with id=AA9, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AB1, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AB2, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.543A pdb=" N PHE B 90 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 123 through 124 412 hydrogen bonds defined for protein. 1164 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: 1.30 Time building geometry restraints manager: 0.83 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: 1743 1.31 - 1.43: 2704 1.43 - 1.56: 6187 1.56 - 1.69: 58 1.69 - 1.81: 84 Bond restraints: 10776 Sorted by residual: bond pdb=" CAI Y01 C1501 " pdb=" CAZ Y01 C1501 " ideal model delta sigma weight residual 1.332 1.553 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CAI Y01 B 401 " pdb=" CAZ Y01 B 401 " ideal model delta sigma weight residual 1.332 1.551 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CAI Y01 A1109 " pdb=" CAZ Y01 A1109 " ideal model delta sigma weight residual 1.332 1.551 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CAI Y01 A1108 " pdb=" CAZ Y01 A1108 " ideal model delta sigma weight residual 1.332 1.550 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CAI Y01 A1106 " pdb=" CAZ Y01 A1106 " ideal model delta sigma weight residual 1.332 1.550 -0.218 2.00e-02 2.50e+03 1.19e+02 ... (remaining 10771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 14436 4.52 - 9.04: 166 9.04 - 13.57: 24 13.57 - 18.09: 0 18.09 - 22.61: 1 Bond angle restraints: 14627 Sorted by residual: angle pdb=" N LYS A 727 " pdb=" CA LYS A 727 " pdb=" C LYS A 727 " ideal model delta sigma weight residual 114.62 105.90 8.72 1.14e+00 7.69e-01 5.85e+01 angle pdb=" O12 PC1 A1110 " pdb=" P PC1 A1110 " pdb=" O14 PC1 A1110 " ideal model delta sigma weight residual 123.67 101.06 22.61 3.00e+00 1.11e-01 5.68e+01 angle pdb=" N MET A 164 " pdb=" CA MET A 164 " pdb=" C MET A 164 " ideal model delta sigma weight residual 113.88 105.08 8.80 1.23e+00 6.61e-01 5.12e+01 angle pdb=" N GLN A 930 " pdb=" CA GLN A 930 " pdb=" C GLN A 930 " ideal model delta sigma weight residual 111.36 105.77 5.59 1.09e+00 8.42e-01 2.63e+01 angle pdb=" C CYS A 464 " pdb=" N GLY A 465 " pdb=" CA GLY A 465 " ideal model delta sigma weight residual 121.41 131.45 -10.04 1.96e+00 2.60e-01 2.62e+01 ... (remaining 14622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 6455 35.40 - 70.80: 210 70.80 - 106.19: 53 106.19 - 141.59: 99 141.59 - 176.99: 18 Dihedral angle restraints: 6835 sinusoidal: 3083 harmonic: 3752 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS A 249 " pdb=" CB CYS A 249 " ideal model delta sinusoidal sigma weight residual -86.00 -174.72 88.72 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CA VAL B 72 " pdb=" C VAL B 72 " pdb=" N ALA B 73 " pdb=" CA ALA B 73 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual 93.00 133.23 -40.23 1 1.00e+01 1.00e-02 2.27e+01 ... (remaining 6832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.197: 1629 1.197 - 2.394: 0 2.394 - 3.591: 0 3.591 - 4.789: 0 4.789 - 5.986: 30 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CBI Y01 A1106 " pdb=" CAU Y01 A1106 " pdb=" CBE Y01 A1106 " pdb=" CBG Y01 A1106 " both_signs ideal model delta sigma weight residual False 2.94 -3.05 5.99 2.00e-01 2.50e+01 8.96e+02 chirality pdb=" CBI Y01 A1107 " pdb=" CAU Y01 A1107 " pdb=" CBE Y01 A1107 " pdb=" CBG Y01 A1107 " both_signs ideal model delta sigma weight residual False 2.94 -3.05 5.98 2.00e-01 2.50e+01 8.95e+02 chirality pdb=" CBI Y01 A1109 " pdb=" CAU Y01 A1109 " pdb=" CBE Y01 A1109 " pdb=" CBG Y01 A1109 " both_signs ideal model delta sigma weight residual False 2.94 -3.05 5.98 2.00e-01 2.50e+01 8.95e+02 ... (remaining 1656 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 243 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO B 244 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 244 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 244 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 132 " 0.049 5.00e-02 4.00e+02 7.32e-02 8.56e+00 pdb=" N PRO B 133 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 163 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C ASN B 163 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN B 163 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP B 164 " 0.016 2.00e-02 2.50e+03 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 64 2.53 - 3.12: 7500 3.12 - 3.71: 15431 3.71 - 4.31: 22190 4.31 - 4.90: 37289 Nonbonded interactions: 82474 Sorted by model distance: nonbonded pdb=" O LEU A 63 " pdb=" OG1 THR A 64 " model vdw 1.934 3.040 nonbonded pdb=" OG SER B 11 " pdb=" N TRP B 12 " model vdw 2.189 3.120 nonbonded pdb=" CA GLY A 195 " pdb=" O VAL A 250 " model vdw 2.215 3.440 nonbonded pdb=" OG SER A 782 " pdb="NA NA A1103 " model vdw 2.220 3.210 nonbonded pdb=" CB ALA B 47 " pdb=" CAC Y01 B 401 " model vdw 2.226 3.880 ... (remaining 82469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.130 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 : 0.013 0.221 10784 Z= 0.609 Angle : 1.285 36.540 14646 Z= 0.636 Chirality : 0.733 5.986 1659 Planarity : 0.007 0.080 1842 Dihedral : 28.018 176.991 4410 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 1.00 % Allowed : 6.72 % Favored : 92.27 % Rotamer: Outliers : 1.07 % Allowed : 8.49 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.99 (0.18), residues: 1294 helix: -2.69 (0.16), residues: 527 sheet: -1.94 (0.36), residues: 142 loop : -2.74 (0.21), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 150 TYR 0.021 0.002 TYR C 21 PHE 0.022 0.002 PHE B 295 TRP 0.015 0.002 TRP A 890 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.01274 / 0.60 (10776) covalent geometry : angle 1.20632 / 0.60 (14627) SS BOND : bond 0.07074 / 3.71 ( 5) SS BOND : angle 16.63773 / 9.18 ( 10) hydrogen bonds : bond 0.19099 / 12.90 ( 412) hydrogen bonds : angle 7.04034 / 5.00 ( 1164) link_BETA1-4 : bond 0.00173 / 0.09 ( 1) link_BETA1-4 : angle 2.63084 / 1.37 ( 3) link_NAG-ASN : bond 0.00486 / 0.24 ( 2) link_NAG-ASN : angle 4.46087 / 2.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8730 (pp) cc_final: 0.8506 (pp) REVERT: A 48 LEU cc_start: 0.8025 (tt) cc_final: 0.7724 (mp) REVERT: A 117 ILE cc_start: 0.9122 (mt) cc_final: 0.8914 (mt) REVERT: A 212 LYS cc_start: 0.7652 (mptt) cc_final: 0.7300 (mtpp) REVERT: A 244 PHE cc_start: 0.7907 (m-80) cc_final: 0.7347 (m-10) REVERT: B 13 LYS cc_start: 0.4944 (OUTLIER) cc_final: 0.4653 (tppt) REVERT: B 51 ILE cc_start: 0.8902 (mm) cc_final: 0.8518 (mt) REVERT: B 80 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8184 (tp) outliers start: 12 outliers final: 5 residues processed: 166 average time/residue: 0.1178 time to fit residues: 25.6573 Evaluate side-chains 98 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 241 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 150 GLN A 163 ASN A 209 ASN A 248 ASN A 406 GLN A 429 ASN A 437 GLN A 503 HIS A 524 HIS A 540 ASN A 570 GLN A 744 GLN A 861 GLN A 882 HIS A 930 GLN B 18 ASN B 69 GLN B 104 ASN B 207 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.130433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085906 restraints weight = 18618.207| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.46 r_work: 0.2931 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10784 Z= 0.133 Angle : 1.611 33.465 14646 Z= 0.586 Chirality : 0.155 1.992 1659 Planarity : 0.005 0.045 1842 Dihedral : 31.716 179.069 1959 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.26 % Favored : 93.43 % Rotamer: Outliers : 2.06 % Allowed : 11.62 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.22), residues: 1294 helix: -0.62 (0.22), residues: 545 sheet: -1.71 (0.36), residues: 149 loop : -2.31 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 173 TYR 0.016 0.001 TYR C 21 PHE 0.031 0.001 PHE A 870 TRP 0.015 0.001 TRP A 89 HIS 0.005 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10776) covalent geometry : angle 1.61062 / 0.59 (14627) SS BOND : bond 0.00218 / 0.11 ( 5) SS BOND : angle 1.79921 / 1.06 ( 10) hydrogen bonds : bond 0.04405 / 3.01 ( 412) hydrogen bonds : angle 4.57885 / 3.31 ( 1164) link_BETA1-4 : bond 0.00234 / 0.12 ( 1) link_BETA1-4 : angle 1.65692 / 0.85 ( 3) link_NAG-ASN : bond 0.00140 / 0.07 ( 2) link_NAG-ASN : angle 2.87995 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 118 GLN cc_start: 0.8849 (tt0) cc_final: 0.8589 (tt0) REVERT: A 126 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7778 (tm-30) REVERT: A 173 ARG cc_start: 0.6507 (mtt90) cc_final: 0.6170 (mtt90) REVERT: A 178 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7467 (pmm) REVERT: A 244 PHE cc_start: 0.8161 (m-80) cc_final: 0.7509 (m-10) REVERT: A 269 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7259 (mmt90) REVERT: A 507 MET cc_start: 0.5675 (tpt) cc_final: 0.5337 (tpt) REVERT: A 513 ARG cc_start: 0.8199 (tpp80) cc_final: 0.7625 (mmp80) REVERT: A 592 ILE cc_start: 0.8785 (tp) cc_final: 0.8494 (tp) REVERT: A 933 ASP cc_start: 0.9097 (t0) cc_final: 0.8843 (t0) REVERT: B 80 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8579 (tp) REVERT: B 119 ASP cc_start: 0.7687 (t0) cc_final: 0.7155 (t0) REVERT: B 290 ARG cc_start: 0.9104 (mmm-85) cc_final: 0.8789 (mmm-85) outliers start: 23 outliers final: 6 residues processed: 114 average time/residue: 0.1060 time to fit residues: 17.3634 Evaluate side-chains 91 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 120 optimal weight: 0.0060 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN A 502 GLN A 524 HIS A 861 GLN B 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.129724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.084599 restraints weight = 18617.107| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.46 r_work: 0.2909 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10784 Z= 0.134 Angle : 1.582 33.972 14646 Z= 0.571 Chirality : 0.156 1.877 1659 Planarity : 0.004 0.050 1842 Dihedral : 31.583 178.576 1945 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.72 % Favored : 94.13 % Rotamer: Outliers : 1.88 % Allowed : 12.87 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.45 (0.23), residues: 1294 helix: 0.27 (0.23), residues: 544 sheet: -1.41 (0.39), residues: 143 loop : -2.02 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 136 TYR 0.015 0.001 TYR C 21 PHE 0.024 0.001 PHE A 870 TRP 0.016 0.001 TRP A 89 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (10776) covalent geometry : angle 1.58190 / 0.57 (14627) SS BOND : bond 0.00248 / 0.13 ( 5) SS BOND : angle 1.55316 / 0.93 ( 10) hydrogen bonds : bond 0.04110 / 2.80 ( 412) hydrogen bonds : angle 4.20563 / 3.03 ( 1164) link_BETA1-4 : bond 0.00416 / 0.22 ( 1) link_BETA1-4 : angle 1.09502 / 0.56 ( 3) link_NAG-ASN : bond 0.00172 / 0.09 ( 2) link_NAG-ASN : angle 2.65350 / 1.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8552 (pp) REVERT: A 118 GLN cc_start: 0.8912 (tt0) cc_final: 0.8662 (tt0) REVERT: A 126 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7805 (tm-30) REVERT: A 173 ARG cc_start: 0.6478 (mtt90) cc_final: 0.6209 (mtt90) REVERT: A 178 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7568 (pmm) REVERT: A 244 PHE cc_start: 0.8148 (m-80) cc_final: 0.7529 (m-10) REVERT: A 390 HIS cc_start: 0.7843 (m170) cc_final: 0.7631 (m90) REVERT: A 507 MET cc_start: 0.5717 (tpt) cc_final: 0.5318 (tpt) REVERT: A 513 ARG cc_start: 0.8134 (tpp80) cc_final: 0.7628 (mmm-85) REVERT: A 539 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8308 (tp-100) REVERT: A 591 MET cc_start: 0.8432 (ptp) cc_final: 0.7809 (ptp) REVERT: A 711 ILE cc_start: 0.8363 (mm) cc_final: 0.8106 (mm) REVERT: B 80 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8606 (tp) REVERT: B 119 ASP cc_start: 0.7984 (t0) cc_final: 0.7399 (t70) outliers start: 21 outliers final: 9 residues processed: 101 average time/residue: 0.0850 time to fit residues: 12.6053 Evaluate side-chains 92 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 204 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 38 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 896 ASN A 905 GLN B 104 ASN B 141 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.082686 restraints weight = 18694.210| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.43 r_work: 0.2868 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10784 Z= 0.170 Angle : 1.591 34.265 14646 Z= 0.575 Chirality : 0.155 1.871 1659 Planarity : 0.004 0.052 1842 Dihedral : 31.553 179.387 1941 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.87 % Favored : 93.97 % Rotamer: Outliers : 1.70 % Allowed : 14.48 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.00 (0.23), residues: 1294 helix: 0.70 (0.24), residues: 539 sheet: -1.22 (0.40), residues: 143 loop : -1.81 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 136 TYR 0.017 0.001 TYR C 21 PHE 0.023 0.001 PHE A 870 TRP 0.011 0.001 TRP B 12 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (10776) covalent geometry : angle 1.59076 / 0.58 (14627) SS BOND : bond 0.00456 / 0.24 ( 5) SS BOND : angle 1.84407 / 1.10 ( 10) hydrogen bonds : bond 0.04455 / 3.06 ( 412) hydrogen bonds : angle 4.14876 / 3.00 ( 1164) link_BETA1-4 : bond 0.00585 / 0.31 ( 1) link_BETA1-4 : angle 0.88539 / 0.46 ( 3) link_NAG-ASN : bond 0.00196 / 0.10 ( 2) link_NAG-ASN : angle 2.58131 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.414 Fit side-chains REVERT: A 46 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8449 (pp) REVERT: A 118 GLN cc_start: 0.8896 (tt0) cc_final: 0.8676 (tt0) REVERT: A 122 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7234 (tp30) REVERT: A 126 GLN cc_start: 0.8499 (tm-30) cc_final: 0.7831 (tm-30) REVERT: A 178 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7378 (pmm) REVERT: A 180 ILE cc_start: 0.7869 (mt) cc_final: 0.7534 (mt) REVERT: A 244 PHE cc_start: 0.8182 (m-80) cc_final: 0.7563 (m-10) REVERT: A 507 MET cc_start: 0.5848 (tpt) cc_final: 0.5481 (tpt) REVERT: A 583 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8017 (mt) REVERT: A 711 ILE cc_start: 0.8344 (mm) cc_final: 0.8083 (mm) REVERT: A 748 MET cc_start: 0.9060 (ttm) cc_final: 0.8648 (ttp) REVERT: A 933 ASP cc_start: 0.9147 (t0) cc_final: 0.8930 (t0) REVERT: B 80 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8530 (tp) REVERT: B 119 ASP cc_start: 0.8234 (t0) cc_final: 0.7613 (t0) REVERT: B 141 HIS cc_start: 0.7235 (OUTLIER) cc_final: 0.7002 (t-90) REVERT: B 202 MET cc_start: 0.6984 (pmm) cc_final: 0.6313 (ptt) outliers start: 19 outliers final: 9 residues processed: 96 average time/residue: 0.0954 time to fit residues: 13.8064 Evaluate side-chains 88 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.130533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.085554 restraints weight = 18349.795| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.42 r_work: 0.2918 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10784 Z= 0.106 Angle : 1.569 33.457 14646 Z= 0.560 Chirality : 0.157 1.882 1659 Planarity : 0.004 0.051 1842 Dihedral : 31.397 179.658 1941 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.67 % Rotamer: Outliers : 1.97 % Allowed : 15.10 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.66 (0.24), residues: 1294 helix: 1.02 (0.24), residues: 544 sheet: -1.05 (0.41), residues: 145 loop : -1.68 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.013 0.001 TYR C 21 PHE 0.018 0.001 PHE A 870 TRP 0.010 0.001 TRP A 89 HIS 0.023 0.001 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10776) covalent geometry : angle 1.56816 / 0.56 (14627) SS BOND : bond 0.00164 / 0.08 ( 5) SS BOND : angle 1.73782 / 1.04 ( 10) hydrogen bonds : bond 0.03552 / 2.42 ( 412) hydrogen bonds : angle 3.91218 / 2.82 ( 1164) link_BETA1-4 : bond 0.00146 / 0.08 ( 1) link_BETA1-4 : angle 0.85508 / 0.44 ( 3) link_NAG-ASN : bond 0.00166 / 0.09 ( 2) link_NAG-ASN : angle 2.26947 / 1.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.409 Fit side-chains REVERT: A 41 MET cc_start: 0.2940 (tmm) cc_final: 0.2244 (mmm) REVERT: A 46 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8572 (pp) REVERT: A 48 LEU cc_start: 0.7745 (tt) cc_final: 0.7451 (mp) REVERT: A 118 GLN cc_start: 0.8916 (tt0) cc_final: 0.8660 (tt0) REVERT: A 122 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7270 (tp30) REVERT: A 126 GLN cc_start: 0.8538 (tm-30) cc_final: 0.7850 (tm-30) REVERT: A 178 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7452 (pmm) REVERT: A 244 PHE cc_start: 0.8167 (m-80) cc_final: 0.7558 (m-10) REVERT: A 507 MET cc_start: 0.5669 (tpt) cc_final: 0.5391 (tpt) REVERT: A 711 ILE cc_start: 0.8308 (mm) cc_final: 0.8078 (mm) REVERT: A 748 MET cc_start: 0.8996 (ttm) cc_final: 0.8585 (ttp) REVERT: B 13 LYS cc_start: 0.4624 (OUTLIER) cc_final: 0.4262 (tppt) REVERT: B 119 ASP cc_start: 0.8189 (t0) cc_final: 0.7539 (t0) REVERT: B 125 ASP cc_start: 0.8493 (t70) cc_final: 0.7994 (t0) REVERT: B 202 MET cc_start: 0.7020 (pmm) cc_final: 0.6707 (ptt) outliers start: 22 outliers final: 11 residues processed: 107 average time/residue: 0.0892 time to fit residues: 14.6985 Evaluate side-chains 95 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 27 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 121 optimal weight: 0.0470 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.131771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.086881 restraints weight = 18469.310| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.43 r_work: 0.2947 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10784 Z= 0.102 Angle : 1.565 33.460 14646 Z= 0.557 Chirality : 0.157 1.890 1659 Planarity : 0.003 0.050 1842 Dihedral : 31.301 179.956 1939 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.72 % Favored : 94.20 % Rotamer: Outliers : 2.14 % Allowed : 15.37 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.32 (0.24), residues: 1294 helix: 1.35 (0.24), residues: 531 sheet: -0.74 (0.43), residues: 142 loop : -1.52 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.012 0.001 TYR A 869 PHE 0.014 0.001 PHE A 870 TRP 0.009 0.001 TRP A 89 HIS 0.004 0.000 HIS B 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (10776) covalent geometry : angle 1.56472 / 0.56 (14627) SS BOND : bond 0.00242 / 0.12 ( 5) SS BOND : angle 1.81813 / 0.96 ( 10) hydrogen bonds : bond 0.03268 / 2.22 ( 412) hydrogen bonds : angle 3.73835 / 2.68 ( 1164) link_BETA1-4 : bond 0.00378 / 0.20 ( 1) link_BETA1-4 : angle 1.04497 / 0.55 ( 3) link_NAG-ASN : bond 0.00145 / 0.08 ( 2) link_NAG-ASN : angle 2.11981 / 1.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.396 Fit side-chains REVERT: A 46 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8481 (pp) REVERT: A 48 LEU cc_start: 0.7830 (tt) cc_final: 0.7492 (mp) REVERT: A 118 GLN cc_start: 0.8948 (tt0) cc_final: 0.8694 (tt0) REVERT: A 122 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7293 (tp30) REVERT: A 126 GLN cc_start: 0.8584 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 178 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7375 (pmm) REVERT: A 244 PHE cc_start: 0.8110 (m-80) cc_final: 0.7696 (m-80) REVERT: A 504 LEU cc_start: 0.6454 (tt) cc_final: 0.6154 (tt) REVERT: A 507 MET cc_start: 0.6038 (tpt) cc_final: 0.5585 (tpt) REVERT: B 13 LYS cc_start: 0.4614 (OUTLIER) cc_final: 0.4217 (tppt) REVERT: B 119 ASP cc_start: 0.8176 (t0) cc_final: 0.7532 (t70) REVERT: B 125 ASP cc_start: 0.8579 (t70) cc_final: 0.8068 (t0) outliers start: 24 outliers final: 11 residues processed: 107 average time/residue: 0.0838 time to fit residues: 13.8603 Evaluate side-chains 94 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 2 optimal weight: 0.0980 chunk 89 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 126 optimal weight: 0.0070 chunk 58 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 ASN B 141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.088647 restraints weight = 18458.556| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.61 r_work: 0.2928 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10784 Z= 0.103 Angle : 1.564 33.454 14646 Z= 0.557 Chirality : 0.157 1.893 1659 Planarity : 0.003 0.050 1842 Dihedral : 31.248 179.524 1939 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.51 % Rotamer: Outliers : 1.25 % Allowed : 15.82 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.11 (0.24), residues: 1294 helix: 1.54 (0.24), residues: 531 sheet: -0.51 (0.44), residues: 141 loop : -1.45 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.015 0.001 TYR C 20 PHE 0.016 0.001 PHE B 15 TRP 0.019 0.001 TRP B 12 HIS 0.002 0.000 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (10776) covalent geometry : angle 1.56378 / 0.56 (14627) SS BOND : bond 0.00177 / 0.09 ( 5) SS BOND : angle 1.85042 / 0.97 ( 10) hydrogen bonds : bond 0.03229 / 2.19 ( 412) hydrogen bonds : angle 3.68215 / 2.64 ( 1164) link_BETA1-4 : bond 0.00341 / 0.18 ( 1) link_BETA1-4 : angle 1.00897 / 0.52 ( 3) link_NAG-ASN : bond 0.00147 / 0.08 ( 2) link_NAG-ASN : angle 2.04464 / 1.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.407 Fit side-chains REVERT: A 46 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8445 (pp) REVERT: A 48 LEU cc_start: 0.7833 (tt) cc_final: 0.7500 (mt) REVERT: A 118 GLN cc_start: 0.8930 (tt0) cc_final: 0.8692 (tt0) REVERT: A 122 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7205 (tp30) REVERT: A 126 GLN cc_start: 0.8570 (tm-30) cc_final: 0.7896 (tm-30) REVERT: A 244 PHE cc_start: 0.8074 (m-80) cc_final: 0.7621 (m-80) REVERT: A 504 LEU cc_start: 0.6041 (tt) cc_final: 0.5795 (tt) REVERT: A 711 ILE cc_start: 0.8094 (mm) cc_final: 0.7775 (mm) REVERT: B 119 ASP cc_start: 0.8086 (t0) cc_final: 0.7511 (t70) REVERT: B 125 ASP cc_start: 0.8409 (t70) cc_final: 0.7899 (t0) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.0787 time to fit residues: 12.0884 Evaluate side-chains 90 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 115 optimal weight: 0.0370 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 46 optimal weight: 0.0670 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN B 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.131184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.086283 restraints weight = 18405.269| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.41 r_work: 0.2939 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10784 Z= 0.110 Angle : 1.567 33.568 14646 Z= 0.559 Chirality : 0.157 1.893 1659 Planarity : 0.003 0.049 1842 Dihedral : 31.211 179.991 1939 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.51 % Rotamer: Outliers : 1.61 % Allowed : 15.37 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.01 (0.24), residues: 1294 helix: 1.60 (0.24), residues: 531 sheet: -0.48 (0.43), residues: 147 loop : -1.37 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.013 0.001 TYR C 21 PHE 0.014 0.001 PHE B 15 TRP 0.017 0.001 TRP B 12 HIS 0.002 0.000 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10776) covalent geometry : angle 1.56647 / 0.56 (14627) SS BOND : bond 0.00234 / 0.12 ( 5) SS BOND : angle 1.81636 / 0.97 ( 10) hydrogen bonds : bond 0.03376 / 2.29 ( 412) hydrogen bonds : angle 3.68710 / 2.64 ( 1164) link_BETA1-4 : bond 0.00359 / 0.19 ( 1) link_BETA1-4 : angle 0.94619 / 0.49 ( 3) link_NAG-ASN : bond 0.00143 / 0.08 ( 2) link_NAG-ASN : angle 2.00281 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.389 Fit side-chains REVERT: A 46 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8453 (pp) REVERT: A 48 LEU cc_start: 0.7784 (tt) cc_final: 0.7427 (mt) REVERT: A 118 GLN cc_start: 0.8956 (tt0) cc_final: 0.8619 (tt0) REVERT: A 122 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: A 126 GLN cc_start: 0.8669 (tm-30) cc_final: 0.7947 (tm-30) REVERT: A 244 PHE cc_start: 0.8154 (m-80) cc_final: 0.7696 (m-80) REVERT: A 269 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7473 (mmt90) REVERT: A 504 LEU cc_start: 0.6194 (tt) cc_final: 0.5970 (tt) REVERT: A 507 MET cc_start: 0.5639 (tpt) cc_final: 0.5148 (tpt) REVERT: A 593 ASP cc_start: 0.7872 (t0) cc_final: 0.7665 (t0) REVERT: B 119 ASP cc_start: 0.8188 (t0) cc_final: 0.7549 (t70) REVERT: B 125 ASP cc_start: 0.8614 (t70) cc_final: 0.8101 (t0) outliers start: 18 outliers final: 12 residues processed: 99 average time/residue: 0.0750 time to fit residues: 11.8292 Evaluate side-chains 94 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 18 optimal weight: 8.9990 chunk 4 optimal weight: 0.2980 chunk 31 optimal weight: 0.2980 chunk 44 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 chunk 124 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 0.0040 chunk 92 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.133554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.089507 restraints weight = 18474.491| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.40 r_work: 0.2992 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10784 Z= 0.098 Angle : 1.557 33.349 14646 Z= 0.553 Chirality : 0.158 1.898 1659 Planarity : 0.003 0.049 1842 Dihedral : 31.138 179.558 1939 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Rotamer: Outliers : 1.34 % Allowed : 16.35 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.13 (0.24), residues: 1294 helix: 1.74 (0.24), residues: 530 sheet: -0.31 (0.43), residues: 146 loop : -1.33 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.011 0.001 TYR A 869 PHE 0.012 0.001 PHE B 15 TRP 0.012 0.001 TRP B 12 HIS 0.002 0.000 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (10776) covalent geometry : angle 1.55674 / 0.55 (14627) SS BOND : bond 0.00174 / 0.09 ( 5) SS BOND : angle 1.48934 / 0.76 ( 10) hydrogen bonds : bond 0.02836 / 1.90 ( 412) hydrogen bonds : angle 3.56030 / 2.55 ( 1164) link_BETA1-4 : bond 0.00364 / 0.19 ( 1) link_BETA1-4 : angle 1.04210 / 0.54 ( 3) link_NAG-ASN : bond 0.00216 / 0.11 ( 2) link_NAG-ASN : angle 1.78167 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.283 Fit side-chains REVERT: A 46 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8428 (pp) REVERT: A 118 GLN cc_start: 0.8935 (tt0) cc_final: 0.8651 (tt0) REVERT: A 126 GLN cc_start: 0.8645 (tm-30) cc_final: 0.7940 (tm-30) REVERT: A 167 GLN cc_start: 0.7070 (mm-40) cc_final: 0.6657 (tp40) REVERT: A 244 PHE cc_start: 0.8170 (m-80) cc_final: 0.7633 (m-10) REVERT: A 269 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7429 (mmt90) REVERT: A 504 LEU cc_start: 0.6321 (tt) cc_final: 0.6106 (tt) REVERT: A 507 MET cc_start: 0.5580 (tpt) cc_final: 0.5093 (tpt) REVERT: B 79 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.7817 (pp30) REVERT: B 119 ASP cc_start: 0.8069 (t0) cc_final: 0.7491 (t70) REVERT: B 125 ASP cc_start: 0.8570 (t70) cc_final: 0.8125 (t0) REVERT: B 294 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7336 (ptm-80) outliers start: 15 outliers final: 7 residues processed: 105 average time/residue: 0.0721 time to fit residues: 11.6556 Evaluate side-chains 94 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 119 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.086725 restraints weight = 18407.431| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.39 r_work: 0.2939 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10784 Z= 0.116 Angle : 1.567 33.613 14646 Z= 0.560 Chirality : 0.157 1.898 1659 Planarity : 0.003 0.050 1842 Dihedral : 31.097 178.985 1939 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.13 % Rotamer: Outliers : 1.16 % Allowed : 17.16 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.18 (0.24), residues: 1294 helix: 1.75 (0.24), residues: 528 sheet: -0.23 (0.44), residues: 146 loop : -1.29 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.012 0.001 TYR A 869 PHE 0.013 0.001 PHE A 538 TRP 0.015 0.001 TRP A 931 HIS 0.002 0.000 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10776) covalent geometry : angle 1.56717 / 0.56 (14627) SS BOND : bond 0.00249 / 0.13 ( 5) SS BOND : angle 1.61180 / 0.89 ( 10) hydrogen bonds : bond 0.03384 / 2.29 ( 412) hydrogen bonds : angle 3.63719 / 2.60 ( 1164) link_BETA1-4 : bond 0.00373 / 0.20 ( 1) link_BETA1-4 : angle 0.93771 / 0.48 ( 3) link_NAG-ASN : bond 0.00149 / 0.08 ( 2) link_NAG-ASN : angle 1.82726 / 0.90 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.416 Fit side-chains REVERT: A 46 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8465 (pp) REVERT: A 48 LEU cc_start: 0.7849 (tt) cc_final: 0.7499 (mt) REVERT: A 118 GLN cc_start: 0.8900 (tt0) cc_final: 0.8663 (tt0) REVERT: A 126 GLN cc_start: 0.8666 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 244 PHE cc_start: 0.8214 (m-80) cc_final: 0.7670 (m-10) REVERT: A 269 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7430 (mmt90) REVERT: A 504 LEU cc_start: 0.6320 (tt) cc_final: 0.6109 (tt) REVERT: A 507 MET cc_start: 0.5588 (tpt) cc_final: 0.5097 (tpt) REVERT: A 591 MET cc_start: 0.8322 (ptp) cc_final: 0.8055 (ptp) REVERT: B 119 ASP cc_start: 0.8179 (t0) cc_final: 0.7613 (t70) REVERT: B 125 ASP cc_start: 0.8623 (t70) cc_final: 0.8144 (t0) REVERT: B 294 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7385 (ptm-80) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.0825 time to fit residues: 11.7701 Evaluate side-chains 89 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 22 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.130417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.085425 restraints weight = 18392.437| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.38 r_work: 0.2919 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10784 Z= 0.123 Angle : 1.570 33.607 14646 Z= 0.562 Chirality : 0.157 1.895 1659 Planarity : 0.004 0.049 1842 Dihedral : 31.102 178.813 1939 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.41 % Favored : 94.44 % Rotamer: Outliers : 1.07 % Allowed : 17.16 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.24), residues: 1294 helix: 1.74 (0.24), residues: 527 sheet: -0.16 (0.44), residues: 146 loop : -1.25 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.013 0.001 TYR A 869 PHE 0.014 0.001 PHE A 538 TRP 0.015 0.001 TRP B 12 HIS 0.002 0.000 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (10776) covalent geometry : angle 1.57009 / 0.56 (14627) SS BOND : bond 0.00245 / 0.13 ( 5) SS BOND : angle 1.65820 / 0.93 ( 10) hydrogen bonds : bond 0.03633 / 2.47 ( 412) hydrogen bonds : angle 3.69033 / 2.64 ( 1164) link_BETA1-4 : bond 0.00419 / 0.22 ( 1) link_BETA1-4 : angle 0.82463 / 0.42 ( 3) link_NAG-ASN : bond 0.00165 / 0.09 ( 2) link_NAG-ASN : angle 1.84463 / 0.92 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2997.66 seconds wall clock time: 51 minutes 56.14 seconds (3116.14 seconds total)