Starting phenix.real_space_refine on Wed Mar 4 05:04:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e1z_30947/03_2026/7e1z_30947_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e1z_30947/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7e1z_30947/03_2026/7e1z_30947_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e1z_30947/03_2026/7e1z_30947_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e1z_30947/03_2026/7e1z_30947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e1z_30947/03_2026/7e1z_30947.map" } 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-5986/lib/python3.9/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, 199 Unusual residues: {' MG': 1, ' NA': 4, 'PC1': 1, 'Y01': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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: 2.45, per 1000 atoms: 0.23 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: 1.04 Conformation dependent library (CDL) restraints added in 407.8 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: 0.36 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: 1.63 Time building geometry restraints manager: 1.36 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 2.470 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: 0.500 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.650 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 covalent geometry : bond 0.01274 (10776) covalent geometry : angle 1.20632 (14627) SS BOND : bond 0.07074 ( 5) SS BOND : angle 16.63773 ( 10) hydrogen bonds : bond 0.19099 ( 412) hydrogen bonds : angle 7.04034 ( 1164) link_BETA1-4 : bond 0.00173 ( 1) link_BETA1-4 : angle 2.63084 ( 3) link_NAG-ASN : bond 0.00486 ( 2) link_NAG-ASN : angle 4.46087 ( 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 : 0.348 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: 0.1354 time to fit residues: 29.4144 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 : 0.376 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 882 HIS B 18 ASN B 69 GLN B 104 ASN B 207 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.130142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.085684 restraints weight = 18591.706| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.45 r_work: 0.2925 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10784 Z= 0.145 Angle : 1.621 34.179 14646 Z= 0.591 Chirality : 0.153 1.890 1659 Planarity : 0.005 0.046 1842 Dihedral : 31.527 178.801 1959 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.34 % Favored : 93.35 % Rotamer: Outliers : 2.06 % Allowed : 11.26 % Favored : 86.68 % 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: -2.33 (0.21), residues: 1294 helix: -0.63 (0.22), residues: 542 sheet: -1.73 (0.36), residues: 149 loop : -2.36 (0.22), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 173 TYR 0.017 0.001 TYR C 21 PHE 0.031 0.001 PHE A 870 TRP 0.014 0.001 TRP A 89 HIS 0.005 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00306 (10776) covalent geometry : angle 1.62017 (14627) SS BOND : bond 0.00408 ( 5) SS BOND : angle 1.89218 ( 10) hydrogen bonds : bond 0.04626 ( 412) hydrogen bonds : angle 4.63720 ( 1164) link_BETA1-4 : bond 0.00373 ( 1) link_BETA1-4 : angle 1.67168 ( 3) link_NAG-ASN : bond 0.00158 ( 2) link_NAG-ASN : angle 2.98541 ( 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 : 0.392 Fit side-chains REVERT: A 118 GLN cc_start: 0.8845 (tt0) cc_final: 0.8594 (tt0) REVERT: A 126 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 178 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7587 (pmm) REVERT: A 244 PHE cc_start: 0.8138 (m-80) cc_final: 0.7492 (m-10) REVERT: A 269 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7192 (mmt90) REVERT: A 507 MET cc_start: 0.5840 (tpt) cc_final: 0.5553 (tpt) REVERT: A 513 ARG cc_start: 0.8166 (tpp80) cc_final: 0.7605 (mmp80) REVERT: A 592 ILE cc_start: 0.8815 (tp) cc_final: 0.8525 (tp) REVERT: A 933 ASP cc_start: 0.9132 (t0) cc_final: 0.8893 (t0) REVERT: B 80 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8661 (tp) REVERT: B 119 ASP cc_start: 0.7674 (t0) cc_final: 0.7172 (t0) REVERT: B 290 ARG cc_start: 0.9111 (mmm-85) cc_final: 0.8791 (mmm-85) outliers start: 23 outliers final: 5 residues processed: 114 average time/residue: 0.1036 time to fit residues: 17.0448 Evaluate side-chains 88 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 34 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 502 GLN A 524 HIS B 104 ASN B 141 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.129161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.083962 restraints weight = 18612.069| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.45 r_work: 0.2894 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10784 Z= 0.147 Angle : 1.590 34.178 14646 Z= 0.576 Chirality : 0.156 1.870 1659 Planarity : 0.004 0.046 1842 Dihedral : 31.594 178.340 1945 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.72 % Favored : 94.13 % Rotamer: Outliers : 1.97 % Allowed : 12.96 % Favored : 85.08 % 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: -1.47 (0.23), residues: 1294 helix: 0.24 (0.23), residues: 544 sheet: -1.43 (0.39), residues: 143 loop : -2.01 (0.23), residues: 607 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 0.026 0.001 PHE A 870 TRP 0.017 0.001 TRP A 89 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00343 (10776) covalent geometry : angle 1.58883 (14627) SS BOND : bond 0.00449 ( 5) SS BOND : angle 2.04562 ( 10) hydrogen bonds : bond 0.04322 ( 412) hydrogen bonds : angle 4.22972 ( 1164) link_BETA1-4 : bond 0.00534 ( 1) link_BETA1-4 : angle 1.03125 ( 3) link_NAG-ASN : bond 0.00209 ( 2) link_NAG-ASN : angle 2.67514 ( 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 106 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.312 Fit side-chains REVERT: A 46 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8553 (pp) REVERT: A 118 GLN cc_start: 0.8932 (tt0) cc_final: 0.8693 (tt0) REVERT: A 126 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7864 (tm-30) REVERT: A 178 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7525 (pmm) REVERT: A 244 PHE cc_start: 0.8138 (m-80) cc_final: 0.7527 (m-10) REVERT: A 507 MET cc_start: 0.5734 (tpt) cc_final: 0.5325 (tpt) REVERT: A 513 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7626 (mmm-85) REVERT: A 539 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8311 (tp-100) REVERT: A 591 MET cc_start: 0.8450 (ptp) cc_final: 0.7826 (ptp) REVERT: A 711 ILE cc_start: 0.8350 (mm) cc_final: 0.8068 (mm) REVERT: B 80 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8621 (tp) REVERT: B 119 ASP cc_start: 0.8056 (t0) cc_final: 0.7478 (t70) REVERT: B 141 HIS cc_start: 0.7268 (OUTLIER) cc_final: 0.6967 (t-90) outliers start: 22 outliers final: 11 residues processed: 101 average time/residue: 0.0967 time to fit residues: 14.3553 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 : 0.475 ------------------------------------------------------------------------------- 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 241 ASN Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 249 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 806 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 B residue 204 TYR Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 38 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 896 ASN A 905 GLN B 104 ASN B 141 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.082829 restraints weight = 18727.107| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.43 r_work: 0.2878 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2668 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= 0.169 Angle : 1.593 34.272 14646 Z= 0.576 Chirality : 0.155 1.868 1659 Planarity : 0.004 0.048 1842 Dihedral : 31.579 179.564 1941 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.26 % Favored : 93.59 % Rotamer: Outliers : 2.06 % Allowed : 14.39 % Favored : 83.56 % 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: -1.08 (0.23), residues: 1294 helix: 0.65 (0.24), residues: 538 sheet: -1.30 (0.40), residues: 143 loop : -1.84 (0.24), residues: 613 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 0.023 0.001 PHE A 870 TRP 0.016 0.001 TRP A 89 HIS 0.012 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00403 (10776) covalent geometry : angle 1.59183 (14627) SS BOND : bond 0.00210 ( 5) SS BOND : angle 1.96980 ( 10) hydrogen bonds : bond 0.04396 ( 412) hydrogen bonds : angle 4.17561 ( 1164) link_BETA1-4 : bond 0.00446 ( 1) link_BETA1-4 : angle 0.88650 ( 3) link_NAG-ASN : bond 0.00201 ( 2) link_NAG-ASN : angle 2.62780 ( 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: 23 poor density : 76 time to evaluate : 0.395 Fit side-chains REVERT: A 46 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8608 (pp) REVERT: A 118 GLN cc_start: 0.8910 (tt0) cc_final: 0.8690 (tt0) REVERT: A 122 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7231 (tp30) REVERT: A 126 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7834 (tm-30) REVERT: A 180 ILE cc_start: 0.7876 (mt) cc_final: 0.7538 (mt) REVERT: A 244 PHE cc_start: 0.8174 (m-80) cc_final: 0.7567 (m-10) REVERT: A 390 HIS cc_start: 0.7800 (m170) cc_final: 0.7583 (m90) REVERT: A 507 MET cc_start: 0.5640 (tpt) cc_final: 0.5278 (tpt) REVERT: A 539 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8344 (tp-100) REVERT: A 711 ILE cc_start: 0.8374 (mm) cc_final: 0.8110 (mm) REVERT: A 748 MET cc_start: 0.9045 (ttm) cc_final: 0.8646 (ttp) REVERT: B 80 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8546 (tp) REVERT: B 119 ASP cc_start: 0.8205 (t0) cc_final: 0.7597 (t0) outliers start: 23 outliers final: 13 residues processed: 96 average time/residue: 0.0895 time to fit residues: 12.9855 Evaluate side-chains 88 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 241 ASN Chi-restraints excluded: chain A residue 249 CYS 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 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 294 ARG 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: 6.9990 chunk 72 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 60 optimal weight: 0.0170 chunk 1 optimal weight: 20.0000 chunk 18 optimal weight: 0.0000 chunk 96 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 55 optimal weight: 0.0020 chunk 32 optimal weight: 0.7980 overall best weight: 0.3030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.131763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087008 restraints weight = 18380.631| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.42 r_work: 0.2952 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2992 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 : 1.563 33.226 14646 Z= 0.558 Chirality : 0.157 1.891 1659 Planarity : 0.004 0.046 1842 Dihedral : 31.412 179.525 1941 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.51 % Rotamer: Outliers : 1.52 % Allowed : 15.55 % 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: -0.62 (0.24), residues: 1294 helix: 1.07 (0.24), residues: 537 sheet: -1.05 (0.41), residues: 145 loop : -1.63 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.012 0.001 TYR C 21 PHE 0.015 0.001 PHE A 870 TRP 0.017 0.001 TRP A 89 HIS 0.002 0.000 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00217 (10776) covalent geometry : angle 1.56230 (14627) SS BOND : bond 0.00466 ( 5) SS BOND : angle 1.71373 ( 10) hydrogen bonds : bond 0.03288 ( 412) hydrogen bonds : angle 3.87628 ( 1164) link_BETA1-4 : bond 0.00477 ( 1) link_BETA1-4 : angle 1.06414 ( 3) link_NAG-ASN : bond 0.00184 ( 2) link_NAG-ASN : angle 2.25787 ( 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 106 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.380 Fit side-chains REVERT: A 46 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8413 (pp) REVERT: A 48 LEU cc_start: 0.7728 (tt) cc_final: 0.7418 (mp) REVERT: A 118 GLN cc_start: 0.8931 (tt0) cc_final: 0.8672 (tt0) REVERT: A 122 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7216 (tp30) REVERT: A 126 GLN cc_start: 0.8501 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 178 MET cc_start: 0.7788 (mpp) cc_final: 0.7415 (pmm) REVERT: A 244 PHE cc_start: 0.8158 (m-80) cc_final: 0.7741 (m-80) REVERT: A 507 MET cc_start: 0.5664 (tpt) cc_final: 0.5356 (tpt) REVERT: A 539 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8273 (tp-100) REVERT: A 591 MET cc_start: 0.8401 (ptp) cc_final: 0.7638 (ptp) REVERT: B 119 ASP cc_start: 0.8060 (t0) cc_final: 0.7417 (t70) REVERT: B 125 ASP cc_start: 0.8480 (t70) cc_final: 0.7978 (t0) REVERT: B 141 HIS cc_start: 0.7267 (OUTLIER) cc_final: 0.7008 (t-90) REVERT: B 202 MET cc_start: 0.6967 (pmm) cc_final: 0.6556 (ptt) outliers start: 17 outliers final: 6 residues processed: 105 average time/residue: 0.0902 time to fit residues: 14.4584 Evaluate side-chains 88 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 218 LEU Chi-restraints excluded: chain A residue 249 CYS 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 141 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 27 optimal weight: 3.9990 chunk 86 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 chunk 105 optimal weight: 0.0030 chunk 121 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 55 optimal weight: 0.0670 chunk 58 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.3126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.133391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.090428 restraints weight = 18523.737| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.67 r_work: 0.2952 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3262 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= 0.100 Angle : 1.563 33.297 14646 Z= 0.556 Chirality : 0.157 1.887 1659 Planarity : 0.003 0.045 1842 Dihedral : 31.266 179.815 1939 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.51 % Rotamer: Outliers : 1.79 % Allowed : 15.73 % 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: -0.28 (0.24), residues: 1294 helix: 1.40 (0.24), residues: 531 sheet: -0.70 (0.42), residues: 145 loop : -1.52 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.012 0.001 TYR A 869 PHE 0.013 0.001 PHE A 870 TRP 0.014 0.001 TRP A 89 HIS 0.002 0.000 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00215 (10776) covalent geometry : angle 1.56285 (14627) SS BOND : bond 0.00349 ( 5) SS BOND : angle 2.06912 ( 10) hydrogen bonds : bond 0.03012 ( 412) hydrogen bonds : angle 3.71049 ( 1164) link_BETA1-4 : bond 0.00432 ( 1) link_BETA1-4 : angle 1.14324 ( 3) link_NAG-ASN : bond 0.00165 ( 2) link_NAG-ASN : angle 2.07625 ( 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 115 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.416 Fit side-chains REVERT: A 46 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8542 (pp) REVERT: A 48 LEU cc_start: 0.7869 (tt) cc_final: 0.7439 (mp) REVERT: A 51 LEU cc_start: 0.8180 (mp) cc_final: 0.7804 (pp) REVERT: A 118 GLN cc_start: 0.8907 (tt0) cc_final: 0.8573 (tt0) REVERT: A 122 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7272 (tp30) REVERT: A 126 GLN cc_start: 0.8491 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 167 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6833 (tp40) REVERT: A 178 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7393 (pmm) REVERT: A 244 PHE cc_start: 0.8097 (m-80) cc_final: 0.7633 (m-80) REVERT: A 390 HIS cc_start: 0.7659 (m170) cc_final: 0.7406 (m90) REVERT: A 539 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8249 (tp-100) REVERT: B 119 ASP cc_start: 0.7902 (t0) cc_final: 0.7394 (t70) REVERT: B 125 ASP cc_start: 0.8382 (t70) cc_final: 0.7914 (t0) REVERT: B 141 HIS cc_start: 0.7084 (OUTLIER) cc_final: 0.6799 (t-90) REVERT: B 294 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7382 (ptm-80) outliers start: 20 outliers final: 9 residues processed: 112 average time/residue: 0.0814 time to fit residues: 14.2415 Evaluate side-chains 99 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 248 ASN Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 2 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 83 optimal weight: 0.4980 chunk 98 optimal weight: 0.0870 chunk 101 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 GLN 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 = 0.130590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.085505 restraints weight = 18449.543| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.42 r_work: 0.2923 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10784 Z= 0.129 Angle : 1.577 33.800 14646 Z= 0.564 Chirality : 0.156 1.878 1659 Planarity : 0.003 0.043 1842 Dihedral : 31.234 179.487 1939 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.51 % Rotamer: Outliers : 1.88 % Allowed : 15.46 % Favored : 82.66 % 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: 1.51 (0.24), residues: 530 sheet: -0.45 (0.44), residues: 139 loop : -1.46 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.015 0.001 TYR C 21 PHE 0.017 0.001 PHE B 15 TRP 0.014 0.001 TRP A 931 HIS 0.002 0.000 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00302 (10776) covalent geometry : angle 1.57616 (14627) SS BOND : bond 0.00491 ( 5) SS BOND : angle 2.29379 ( 10) hydrogen bonds : bond 0.03672 ( 412) hydrogen bonds : angle 3.78109 ( 1164) link_BETA1-4 : bond 0.00393 ( 1) link_BETA1-4 : angle 0.96351 ( 3) link_NAG-ASN : bond 0.00139 ( 2) link_NAG-ASN : angle 2.16076 ( 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 102 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.406 Fit side-chains REVERT: A 46 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8621 (pp) REVERT: A 48 LEU cc_start: 0.7857 (tt) cc_final: 0.7495 (mt) REVERT: A 118 GLN cc_start: 0.8985 (tt0) cc_final: 0.8743 (tt0) REVERT: A 122 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: A 126 GLN cc_start: 0.8611 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 178 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7305 (pmm) REVERT: A 244 PHE cc_start: 0.8200 (m-80) cc_final: 0.7776 (m-80) REVERT: A 351 MET cc_start: 0.8293 (mtt) cc_final: 0.7995 (mtp) REVERT: A 507 MET cc_start: 0.5791 (tpt) cc_final: 0.5191 (tpt) REVERT: A 539 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8222 (tp-100) REVERT: B 119 ASP cc_start: 0.8200 (t0) cc_final: 0.7565 (t70) REVERT: B 125 ASP cc_start: 0.8624 (t70) cc_final: 0.8160 (t0) REVERT: B 141 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.6937 (t-90) outliers start: 21 outliers final: 14 residues processed: 99 average time/residue: 0.0755 time to fit residues: 11.8805 Evaluate side-chains 95 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 248 ASN Chi-restraints excluded: chain A residue 249 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 730 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 141 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 73 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.126401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.081128 restraints weight = 18448.068| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.36 r_work: 0.2842 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10784 Z= 0.241 Angle : 1.618 34.983 14646 Z= 0.590 Chirality : 0.155 1.869 1659 Planarity : 0.004 0.043 1842 Dihedral : 31.337 179.993 1939 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.26 % Favored : 93.59 % Rotamer: Outliers : 2.23 % Allowed : 15.19 % Favored : 82.57 % 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: -0.42 (0.24), residues: 1294 helix: 1.15 (0.24), residues: 538 sheet: -0.58 (0.43), residues: 139 loop : -1.54 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 294 TYR 0.018 0.002 TYR C 21 PHE 0.023 0.002 PHE A 870 TRP 0.026 0.002 TRP B 12 HIS 0.004 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00586 (10776) covalent geometry : angle 1.61686 (14627) SS BOND : bond 0.00378 ( 5) SS BOND : angle 2.74378 ( 10) hydrogen bonds : bond 0.04949 ( 412) hydrogen bonds : angle 4.11831 ( 1164) link_BETA1-4 : bond 0.00625 ( 1) link_BETA1-4 : angle 0.72633 ( 3) link_NAG-ASN : bond 0.00273 ( 2) link_NAG-ASN : angle 2.47470 ( 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 100 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.334 Fit side-chains REVERT: A 46 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8614 (pp) REVERT: A 48 LEU cc_start: 0.7814 (tt) cc_final: 0.7485 (mt) REVERT: A 118 GLN cc_start: 0.8991 (tt0) cc_final: 0.8774 (tt0) REVERT: A 122 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7300 (tp30) REVERT: A 244 PHE cc_start: 0.8237 (m-80) cc_final: 0.7851 (m-80) REVERT: A 504 LEU cc_start: 0.6378 (tt) cc_final: 0.6129 (tt) REVERT: A 507 MET cc_start: 0.5798 (tpt) cc_final: 0.5265 (tpt) REVERT: A 539 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8262 (tp-100) REVERT: A 933 ASP cc_start: 0.9186 (t0) cc_final: 0.8961 (t0) REVERT: B 51 ILE cc_start: 0.8974 (mm) cc_final: 0.8733 (mt) REVERT: B 119 ASP cc_start: 0.8349 (t0) cc_final: 0.7777 (t0) REVERT: B 141 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.7014 (t-90) outliers start: 25 outliers final: 17 residues processed: 97 average time/residue: 0.0821 time to fit residues: 12.5435 Evaluate side-chains 93 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 174 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 483 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 580 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 141 HIS 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: 7.9990 chunk 4 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.128687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.085693 restraints weight = 18470.388| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.83 r_work: 0.2864 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10784 Z= 0.133 Angle : 1.583 33.603 14646 Z= 0.568 Chirality : 0.157 1.894 1659 Planarity : 0.004 0.044 1842 Dihedral : 31.284 179.264 1939 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.72 % Favored : 94.13 % Rotamer: Outliers : 1.61 % Allowed : 15.91 % 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: -0.23 (0.24), residues: 1294 helix: 1.37 (0.24), residues: 538 sheet: -0.62 (0.42), residues: 147 loop : -1.47 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.014 0.001 TYR C 21 PHE 0.017 0.001 PHE A 870 TRP 0.025 0.001 TRP A 89 HIS 0.002 0.000 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00308 (10776) covalent geometry : angle 1.58215 (14627) SS BOND : bond 0.00312 ( 5) SS BOND : angle 2.16718 ( 10) hydrogen bonds : bond 0.03962 ( 412) hydrogen bonds : angle 3.88798 ( 1164) link_BETA1-4 : bond 0.00379 ( 1) link_BETA1-4 : angle 0.71923 ( 3) link_NAG-ASN : bond 0.00164 ( 2) link_NAG-ASN : angle 2.13827 ( 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 94 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.373 Fit side-chains REVERT: A 46 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8666 (pp) REVERT: A 48 LEU cc_start: 0.7863 (tt) cc_final: 0.7441 (mt) REVERT: A 51 LEU cc_start: 0.8322 (mp) cc_final: 0.8102 (mt) REVERT: A 118 GLN cc_start: 0.8953 (tt0) cc_final: 0.8725 (tt0) REVERT: A 122 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: A 126 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8005 (tm-30) REVERT: A 244 PHE cc_start: 0.8138 (m-80) cc_final: 0.7548 (m-10) REVERT: A 504 LEU cc_start: 0.6343 (tt) cc_final: 0.6099 (tt) REVERT: A 507 MET cc_start: 0.5771 (tpt) cc_final: 0.5279 (tpt) REVERT: A 539 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8225 (tp-100) REVERT: B 13 LYS cc_start: 0.4785 (OUTLIER) cc_final: 0.4330 (tppt) REVERT: B 51 ILE cc_start: 0.8915 (mm) cc_final: 0.8656 (mt) REVERT: B 119 ASP cc_start: 0.8262 (t0) cc_final: 0.7727 (t0) REVERT: B 125 ASP cc_start: 0.8316 (t70) cc_final: 0.7837 (t0) outliers start: 18 outliers final: 14 residues processed: 92 average time/residue: 0.0808 time to fit residues: 11.7102 Evaluate side-chains 91 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 248 ASN Chi-restraints excluded: chain A residue 249 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 580 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 119 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 60 optimal weight: 0.0470 overall best weight: 2.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.081481 restraints weight = 18443.665| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.38 r_work: 0.2851 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10784 Z= 0.201 Angle : 1.608 34.490 14646 Z= 0.583 Chirality : 0.155 1.891 1659 Planarity : 0.004 0.044 1842 Dihedral : 31.270 179.969 1939 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.18 % Favored : 93.66 % Rotamer: Outliers : 1.61 % Allowed : 16.00 % Favored : 82.39 % 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: -0.33 (0.24), residues: 1294 helix: 1.24 (0.24), residues: 540 sheet: -0.70 (0.42), residues: 147 loop : -1.47 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.017 0.001 TYR C 21 PHE 0.021 0.001 PHE A 870 TRP 0.025 0.002 TRP B 12 HIS 0.003 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00484 (10776) covalent geometry : angle 1.60707 (14627) SS BOND : bond 0.00433 ( 5) SS BOND : angle 2.50671 ( 10) hydrogen bonds : bond 0.04637 ( 412) hydrogen bonds : angle 4.04216 ( 1164) link_BETA1-4 : bond 0.00398 ( 1) link_BETA1-4 : angle 0.69647 ( 3) link_NAG-ASN : bond 0.00240 ( 2) link_NAG-ASN : angle 2.25904 ( 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 93 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.438 Fit side-chains REVERT: A 46 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8682 (pp) REVERT: A 118 GLN cc_start: 0.8975 (tt0) cc_final: 0.8763 (tt0) REVERT: A 122 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7314 (tp30) REVERT: A 126 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8033 (tm-30) REVERT: A 244 PHE cc_start: 0.8239 (m-80) cc_final: 0.7640 (m-10) REVERT: A 504 LEU cc_start: 0.6261 (tt) cc_final: 0.5984 (tt) REVERT: A 507 MET cc_start: 0.5855 (tpt) cc_final: 0.5336 (tpt) REVERT: A 539 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8252 (tp-100) REVERT: A 933 ASP cc_start: 0.9168 (t0) cc_final: 0.8953 (t0) REVERT: B 13 LYS cc_start: 0.4851 (OUTLIER) cc_final: 0.4356 (tppt) REVERT: B 51 ILE cc_start: 0.8964 (mm) cc_final: 0.8728 (mt) REVERT: B 119 ASP cc_start: 0.8370 (t0) cc_final: 0.7803 (t0) REVERT: B 125 ASP cc_start: 0.8566 (t70) cc_final: 0.8159 (t0) REVERT: B 141 HIS cc_start: 0.7378 (t-90) cc_final: 0.6930 (t-170) outliers start: 18 outliers final: 15 residues processed: 91 average time/residue: 0.0802 time to fit residues: 11.6218 Evaluate side-chains 92 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 248 ASN Chi-restraints excluded: chain A residue 249 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 580 ILE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 28 THR 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 22 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.129878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.087226 restraints weight = 18359.124| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.73 r_work: 0.2893 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3516 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= 0.109 Angle : 1.572 33.297 14646 Z= 0.562 Chirality : 0.158 1.909 1659 Planarity : 0.004 0.044 1842 Dihedral : 31.208 179.756 1939 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.51 % Rotamer: Outliers : 1.52 % Allowed : 16.35 % Favored : 82.13 % 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: -0.51 (0.43), residues: 147 loop : -1.37 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.013 0.001 TYR C 21 PHE 0.011 0.001 PHE B 15 TRP 0.022 0.001 TRP A 89 HIS 0.002 0.000 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00241 (10776) covalent geometry : angle 1.57148 (14627) SS BOND : bond 0.00268 ( 5) SS BOND : angle 1.91356 ( 10) hydrogen bonds : bond 0.03528 ( 412) hydrogen bonds : angle 3.77128 ( 1164) link_BETA1-4 : bond 0.00524 ( 1) link_BETA1-4 : angle 0.85838 ( 3) link_NAG-ASN : bond 0.00192 ( 2) link_NAG-ASN : angle 1.94982 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2905.32 seconds wall clock time: 50 minutes 12.78 seconds (3012.78 seconds total)