Starting phenix.real_space_refine on Tue Jul 29 05:47:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e1z_30947/07_2025/7e1z_30947_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e1z_30947/07_2025/7e1z_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_2025/7e1z_30947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e1z_30947/07_2025/7e1z_30947.map" model { file = "/net/cci-nas-00/data/ceres_data/7e1z_30947/07_2025/7e1z_30947_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e1z_30947/07_2025/7e1z_30947_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.65, per 1000 atoms: 0.63 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: 2.57 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.14 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: 3.59 Time building geometry restraints manager: 3.08 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: 10.150 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 27.000 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.870 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.002 TRP A 890 HIS 0.006 0.001 HIS A 52 PHE 0.022 0.002 PHE B 295 TYR 0.021 0.002 TYR C 21 ARG 0.004 0.001 ARG B 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 2) link_NAG-ASN : angle 4.46087 ( 6) link_BETA1-4 : bond 0.00173 ( 1) link_BETA1-4 : angle 2.63084 ( 3) hydrogen bonds : bond 0.19099 ( 412) hydrogen bonds : angle 7.04034 ( 1164) SS BOND : bond 0.07074 ( 5) SS BOND : angle 16.63773 ( 10) covalent geometry : bond 0.01274 (10776) covalent geometry : angle 1.20632 (14627) *********************** 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 : 1.247 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: 0.8185 (tp) outliers start: 12 outliers final: 5 residues processed: 166 average time/residue: 0.3278 time to fit residues: 71.5746 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 : 1.241 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 A 942 ASN B 18 ASN B 69 GLN B 104 ASN B 207 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.129525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.085005 restraints weight = 18362.307| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.44 r_work: 0.2912 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10784 Z= 0.142 Angle : 1.624 34.583 14646 Z= 0.593 Chirality : 0.154 1.970 1659 Planarity : 0.005 0.046 1842 Dihedral : 31.503 179.898 1959 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.18 % Favored : 93.51 % Rotamer: Outliers : 1.97 % Allowed : 11.44 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.21), residues: 1294 helix: -0.64 (0.22), residues: 542 sheet: -1.71 (0.37), residues: 143 loop : -2.35 (0.22), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 89 HIS 0.005 0.001 HIS A 398 PHE 0.031 0.001 PHE A 870 TYR 0.018 0.001 TYR C 21 ARG 0.006 0.000 ARG A 173 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 2) link_NAG-ASN : angle 3.09877 ( 6) link_BETA1-4 : bond 0.00347 ( 1) link_BETA1-4 : angle 1.69035 ( 3) hydrogen bonds : bond 0.04856 ( 412) hydrogen bonds : angle 4.69910 ( 1164) SS BOND : bond 0.00479 ( 5) SS BOND : angle 1.98085 ( 10) covalent geometry : bond 0.00319 (10776) covalent geometry : angle 1.62285 (14627) *********************** 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 114 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.250 Fit side-chains REVERT: A 118 GLN cc_start: 0.8837 (tt0) cc_final: 0.8596 (tt0) REVERT: A 126 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 244 PHE cc_start: 0.8027 (m-80) cc_final: 0.7374 (m-10) REVERT: A 507 MET cc_start: 0.5667 (tpt) cc_final: 0.5403 (tpt) REVERT: A 513 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7564 (mmp80) REVERT: A 592 ILE cc_start: 0.8834 (tp) cc_final: 0.8543 (tp) REVERT: A 933 ASP cc_start: 0.9155 (t0) cc_final: 0.8908 (t0) REVERT: B 80 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 119 ASP cc_start: 0.7686 (t0) cc_final: 0.7201 (t0) REVERT: B 290 ARG cc_start: 0.9126 (mmm-85) cc_final: 0.8806 (mmm-85) outliers start: 22 outliers final: 7 residues processed: 109 average time/residue: 0.2451 time to fit residues: 38.2670 Evaluate side-chains 85 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 241 ASN 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 70 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN A 502 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 = 0.3747 r_free = 0.3747 target = 0.129502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.084424 restraints weight = 18553.894| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.45 r_work: 0.2906 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2526 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= 0.137 Angle : 1.583 34.088 14646 Z= 0.572 Chirality : 0.156 1.880 1659 Planarity : 0.004 0.046 1842 Dihedral : 31.657 179.988 1941 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.80 % Favored : 94.05 % Rotamer: Outliers : 2.14 % Allowed : 12.42 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.23), residues: 1294 helix: 0.26 (0.23), residues: 544 sheet: -1.46 (0.39), residues: 143 loop : -2.02 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 89 HIS 0.002 0.001 HIS A 290 PHE 0.026 0.001 PHE A 870 TYR 0.015 0.001 TYR C 21 ARG 0.006 0.000 ARG A 173 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 2) link_NAG-ASN : angle 2.63639 ( 6) link_BETA1-4 : bond 0.00258 ( 1) link_BETA1-4 : angle 0.94467 ( 3) hydrogen bonds : bond 0.04136 ( 412) hydrogen bonds : angle 4.20196 ( 1164) SS BOND : bond 0.00220 ( 5) SS BOND : angle 1.77100 ( 10) covalent geometry : bond 0.00317 (10776) covalent geometry : angle 1.58274 (14627) *********************** 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 108 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 1.259 Fit side-chains REVERT: A 118 GLN cc_start: 0.8922 (tt0) cc_final: 0.8676 (tt0) REVERT: A 126 GLN cc_start: 0.8413 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 178 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7427 (pmm) REVERT: A 211 CYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6846 (t) REVERT: A 244 PHE cc_start: 0.8147 (m-80) cc_final: 0.7525 (m-10) REVERT: A 507 MET cc_start: 0.5717 (tpt) cc_final: 0.5312 (tpt) REVERT: A 513 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7619 (mmm-85) REVERT: A 539 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8309 (tp-100) REVERT: A 591 MET cc_start: 0.8466 (ptp) cc_final: 0.7845 (ptp) REVERT: A 711 ILE cc_start: 0.8360 (mm) cc_final: 0.8093 (mm) REVERT: A 748 MET cc_start: 0.9028 (ttm) cc_final: 0.8609 (ttp) REVERT: B 13 LYS cc_start: 0.4381 (OUTLIER) cc_final: 0.4072 (tppt) REVERT: B 80 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8614 (tp) REVERT: B 119 ASP cc_start: 0.8031 (t0) cc_final: 0.7443 (t70) REVERT: B 141 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6967 (t-90) outliers start: 24 outliers final: 10 residues processed: 102 average time/residue: 0.2315 time to fit residues: 34.4661 Evaluate side-chains 92 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 122 GLU 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 13 LYS 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 88 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 121 optimal weight: 0.2980 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.130485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.085624 restraints weight = 18293.418| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.43 r_work: 0.2923 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10784 Z= 0.113 Angle : 1.572 33.471 14646 Z= 0.563 Chirality : 0.156 1.872 1659 Planarity : 0.004 0.046 1842 Dihedral : 31.553 179.848 1941 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.80 % Favored : 94.05 % Rotamer: Outliers : 1.97 % Allowed : 14.30 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.23), residues: 1294 helix: 0.77 (0.24), residues: 538 sheet: -1.21 (0.40), residues: 143 loop : -1.76 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 89 HIS 0.008 0.001 HIS B 141 PHE 0.020 0.001 PHE A 870 TYR 0.014 0.001 TYR C 21 ARG 0.007 0.000 ARG A 173 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 2) link_NAG-ASN : angle 2.45524 ( 6) link_BETA1-4 : bond 0.00193 ( 1) link_BETA1-4 : angle 0.96864 ( 3) hydrogen bonds : bond 0.03689 ( 412) hydrogen bonds : angle 4.02601 ( 1164) SS BOND : bond 0.00199 ( 5) SS BOND : angle 1.44102 ( 10) covalent geometry : bond 0.00253 (10776) covalent geometry : angle 1.57125 (14627) *********************** 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 104 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 1.199 Fit side-chains REVERT: A 46 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8656 (pp) REVERT: A 118 GLN cc_start: 0.8920 (tt0) cc_final: 0.8678 (tt0) REVERT: A 126 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 178 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7402 (pmm) REVERT: A 244 PHE cc_start: 0.8152 (m-80) cc_final: 0.7548 (m-10) REVERT: A 390 HIS cc_start: 0.7779 (m170) cc_final: 0.7557 (m90) REVERT: A 507 MET cc_start: 0.5700 (tpt) cc_final: 0.5361 (tpt) REVERT: A 539 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8289 (tp-100) REVERT: A 583 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7953 (mt) REVERT: A 711 ILE cc_start: 0.8294 (mm) cc_final: 0.8048 (mm) REVERT: A 748 MET cc_start: 0.8953 (ttm) cc_final: 0.8551 (ttp) REVERT: B 13 LYS cc_start: 0.4552 (OUTLIER) cc_final: 0.4267 (tppt) REVERT: B 119 ASP cc_start: 0.8031 (t0) cc_final: 0.7451 (t70) outliers start: 22 outliers final: 10 residues processed: 101 average time/residue: 0.2416 time to fit residues: 35.6579 Evaluate side-chains 90 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU 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 241 ASN 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 13 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 162 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 125 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 53 optimal weight: 20.0000 chunk 60 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 HIS 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 = 0.130489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.085463 restraints weight = 18431.643| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.42 r_work: 0.2924 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2925 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= 0.115 Angle : 1.571 33.610 14646 Z= 0.561 Chirality : 0.156 1.877 1659 Planarity : 0.004 0.046 1842 Dihedral : 31.475 179.779 1939 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.13 % Rotamer: Outliers : 1.88 % Allowed : 14.66 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1294 helix: 1.05 (0.24), residues: 538 sheet: -1.06 (0.41), residues: 145 loop : -1.69 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 89 HIS 0.003 0.001 HIS B 141 PHE 0.018 0.001 PHE A 870 TYR 0.014 0.001 TYR C 21 ARG 0.003 0.000 ARG B 136 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 2) link_NAG-ASN : angle 2.34500 ( 6) link_BETA1-4 : bond 0.00249 ( 1) link_BETA1-4 : angle 0.94802 ( 3) hydrogen bonds : bond 0.03645 ( 412) hydrogen bonds : angle 3.90172 ( 1164) SS BOND : bond 0.00268 ( 5) SS BOND : angle 1.68806 ( 10) covalent geometry : bond 0.00262 (10776) covalent geometry : angle 1.57053 (14627) *********************** 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 101 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 1.155 Fit side-chains REVERT: A 41 MET cc_start: 0.2910 (tmm) cc_final: 0.2198 (mmm) REVERT: A 46 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8608 (pp) REVERT: A 48 LEU cc_start: 0.7800 (tt) cc_final: 0.7481 (mp) REVERT: A 118 GLN cc_start: 0.8949 (tt0) cc_final: 0.8711 (tt0) REVERT: A 126 GLN cc_start: 0.8503 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 178 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7472 (pmm) REVERT: A 244 PHE cc_start: 0.8116 (m-80) cc_final: 0.7718 (m-80) REVERT: A 324 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8878 (tp) REVERT: A 390 HIS cc_start: 0.7763 (m170) cc_final: 0.7526 (m90) REVERT: A 507 MET cc_start: 0.5715 (tpt) cc_final: 0.5503 (tpt) REVERT: A 539 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8284 (tp-100) REVERT: A 711 ILE cc_start: 0.8258 (mm) cc_final: 0.8056 (mm) REVERT: A 748 MET cc_start: 0.8966 (ttm) cc_final: 0.8572 (ttp) REVERT: B 13 LYS cc_start: 0.4678 (OUTLIER) cc_final: 0.4384 (tppt) REVERT: B 119 ASP cc_start: 0.8075 (t0) cc_final: 0.7422 (t70) REVERT: B 125 ASP cc_start: 0.8482 (t0) cc_final: 0.8043 (t0) REVERT: B 202 MET cc_start: 0.7088 (pmm) cc_final: 0.6497 (ptt) outliers start: 21 outliers final: 12 residues processed: 99 average time/residue: 0.1986 time to fit residues: 30.1840 Evaluate side-chains 91 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 174 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 324 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 806 THR 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 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 111 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 483 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.127281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.081752 restraints weight = 18460.760| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.39 r_work: 0.2857 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10784 Z= 0.203 Angle : 1.605 34.665 14646 Z= 0.582 Chirality : 0.155 1.870 1659 Planarity : 0.004 0.047 1842 Dihedral : 31.448 179.545 1939 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.57 % Favored : 93.28 % Rotamer: Outliers : 2.41 % Allowed : 14.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1294 helix: 1.02 (0.24), residues: 538 sheet: -0.97 (0.42), residues: 142 loop : -1.66 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 12 HIS 0.003 0.001 HIS A 290 PHE 0.022 0.001 PHE A 870 TYR 0.018 0.001 TYR C 21 ARG 0.004 0.000 ARG A 173 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 2) link_NAG-ASN : angle 2.51083 ( 6) link_BETA1-4 : bond 0.00442 ( 1) link_BETA1-4 : angle 0.73674 ( 3) hydrogen bonds : bond 0.04728 ( 412) hydrogen bonds : angle 4.11349 ( 1164) SS BOND : bond 0.00307 ( 5) SS BOND : angle 2.51887 ( 10) covalent geometry : bond 0.00489 (10776) covalent geometry : angle 1.60361 (14627) *********************** 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 102 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 1.300 Fit side-chains REVERT: A 41 MET cc_start: 0.2947 (tmm) cc_final: 0.2640 (mmm) REVERT: A 46 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8629 (pp) REVERT: A 48 LEU cc_start: 0.7780 (tt) cc_final: 0.7420 (mt) REVERT: A 118 GLN cc_start: 0.8931 (tt0) cc_final: 0.8709 (tt0) REVERT: A 122 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: A 126 GLN cc_start: 0.8617 (tm-30) cc_final: 0.7926 (tm-30) REVERT: A 244 PHE cc_start: 0.8168 (m-80) cc_final: 0.7554 (m-10) REVERT: A 324 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8817 (tp) REVERT: A 492 ILE cc_start: 0.4627 (OUTLIER) cc_final: 0.4397 (tp) REVERT: A 539 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8291 (tp-100) REVERT: A 711 ILE cc_start: 0.8366 (mm) cc_final: 0.8097 (mm) REVERT: A 933 ASP cc_start: 0.9207 (t0) cc_final: 0.8972 (t0) REVERT: B 12 TRP cc_start: 0.5405 (OUTLIER) cc_final: 0.4946 (t60) REVERT: B 13 LYS cc_start: 0.4869 (OUTLIER) cc_final: 0.4380 (tppt) REVERT: B 119 ASP cc_start: 0.8337 (t0) cc_final: 0.7777 (t0) outliers start: 27 outliers final: 16 residues processed: 100 average time/residue: 0.1920 time to fit residues: 30.2246 Evaluate side-chains 94 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 324 LEU Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 492 ILE 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 A residue 806 THR Chi-restraints excluded: chain B residue 12 TRP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 118 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.127836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.082369 restraints weight = 18631.912| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.41 r_work: 0.2867 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10784 Z= 0.166 Angle : 1.589 34.036 14646 Z= 0.573 Chirality : 0.156 1.879 1659 Planarity : 0.004 0.046 1842 Dihedral : 31.369 179.501 1939 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.95 % Favored : 93.89 % Rotamer: Outliers : 2.23 % Allowed : 15.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.24), residues: 1294 helix: 1.11 (0.24), residues: 538 sheet: -0.86 (0.42), residues: 142 loop : -1.62 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 89 HIS 0.003 0.001 HIS A 290 PHE 0.021 0.001 PHE A 870 TYR 0.016 0.001 TYR C 21 ARG 0.003 0.000 ARG A 173 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 2) link_NAG-ASN : angle 2.34720 ( 6) link_BETA1-4 : bond 0.00486 ( 1) link_BETA1-4 : angle 0.74095 ( 3) hydrogen bonds : bond 0.04361 ( 412) hydrogen bonds : angle 4.02837 ( 1164) SS BOND : bond 0.00259 ( 5) SS BOND : angle 2.42215 ( 10) covalent geometry : bond 0.00397 (10776) covalent geometry : angle 1.58823 (14627) *********************** 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: 25 poor density : 77 time to evaluate : 1.237 Fit side-chains REVERT: A 46 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8617 (pp) REVERT: A 48 LEU cc_start: 0.7784 (tt) cc_final: 0.7356 (mt) REVERT: A 118 GLN cc_start: 0.8953 (tt0) cc_final: 0.8739 (tt0) REVERT: A 122 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7346 (tp30) REVERT: A 126 GLN cc_start: 0.8649 (tm-30) cc_final: 0.7940 (tm-30) REVERT: A 244 PHE cc_start: 0.8166 (m-80) cc_final: 0.7554 (m-10) REVERT: A 324 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8807 (tp) REVERT: A 507 MET cc_start: 0.6083 (tpt) cc_final: 0.5653 (tpt) REVERT: A 711 ILE cc_start: 0.8353 (mm) cc_final: 0.8083 (mm) REVERT: A 933 ASP cc_start: 0.9210 (t0) cc_final: 0.8972 (t0) REVERT: B 12 TRP cc_start: 0.5257 (OUTLIER) cc_final: 0.4901 (t60) REVERT: B 13 LYS cc_start: 0.4778 (OUTLIER) cc_final: 0.4418 (tppt) REVERT: B 119 ASP cc_start: 0.8340 (t0) cc_final: 0.7773 (t0) outliers start: 25 outliers final: 15 residues processed: 100 average time/residue: 0.1777 time to fit residues: 27.6526 Evaluate side-chains 95 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 324 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 A residue 730 ILE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 12 TRP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 110 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.084651 restraints weight = 18447.821| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.41 r_work: 0.2905 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3259 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= 0.114 Angle : 1.572 33.523 14646 Z= 0.561 Chirality : 0.157 1.898 1659 Planarity : 0.003 0.045 1842 Dihedral : 31.272 179.655 1939 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.89 % Rotamer: Outliers : 1.97 % Allowed : 15.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1294 helix: 1.43 (0.24), residues: 531 sheet: -0.62 (0.43), residues: 141 loop : -1.47 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 89 HIS 0.002 0.000 HIS A 290 PHE 0.015 0.001 PHE A 870 TYR 0.014 0.001 TYR C 21 ARG 0.003 0.000 ARG A 551 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 2) link_NAG-ASN : angle 2.10322 ( 6) link_BETA1-4 : bond 0.00431 ( 1) link_BETA1-4 : angle 0.82042 ( 3) hydrogen bonds : bond 0.03678 ( 412) hydrogen bonds : angle 3.83150 ( 1164) SS BOND : bond 0.00238 ( 5) SS BOND : angle 1.96409 ( 10) covalent geometry : bond 0.00256 (10776) covalent geometry : angle 1.57115 (14627) *********************** 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 103 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 1.165 Fit side-chains REVERT: A 46 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8646 (pp) REVERT: A 118 GLN cc_start: 0.8970 (tt0) cc_final: 0.8730 (tt0) REVERT: A 122 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7222 (tp30) REVERT: A 126 GLN cc_start: 0.8660 (tm-30) cc_final: 0.7934 (tm-30) REVERT: A 244 PHE cc_start: 0.8144 (m-80) cc_final: 0.7549 (m-10) REVERT: A 324 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8885 (tp) REVERT: A 504 LEU cc_start: 0.6471 (tt) cc_final: 0.6223 (tt) REVERT: A 507 MET cc_start: 0.6040 (tpt) cc_final: 0.5610 (tpt) REVERT: A 711 ILE cc_start: 0.8310 (mm) cc_final: 0.8061 (mm) REVERT: B 13 LYS cc_start: 0.4568 (OUTLIER) cc_final: 0.4078 (tppt) REVERT: B 119 ASP cc_start: 0.8318 (t0) cc_final: 0.7704 (t0) REVERT: B 125 ASP cc_start: 0.8571 (t0) cc_final: 0.8158 (t0) REVERT: B 141 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.6894 (t-90) outliers start: 22 outliers final: 14 residues processed: 100 average time/residue: 0.1870 time to fit residues: 29.3088 Evaluate side-chains 95 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 324 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 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 112 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.129246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.084265 restraints weight = 18545.100| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.39 r_work: 0.2896 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3315 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= 0.126 Angle : 1.575 33.648 14646 Z= 0.564 Chirality : 0.156 1.896 1659 Planarity : 0.004 0.045 1842 Dihedral : 31.258 179.247 1939 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.72 % Favored : 94.20 % Rotamer: Outliers : 1.70 % Allowed : 15.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1294 helix: 1.41 (0.24), residues: 538 sheet: -0.58 (0.42), residues: 147 loop : -1.50 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 89 HIS 0.003 0.000 HIS B 141 PHE 0.015 0.001 PHE A 870 TYR 0.013 0.001 TYR A 869 ARG 0.003 0.000 ARG B 136 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 2) link_NAG-ASN : angle 2.08490 ( 6) link_BETA1-4 : bond 0.00387 ( 1) link_BETA1-4 : angle 0.84440 ( 3) hydrogen bonds : bond 0.03763 ( 412) hydrogen bonds : angle 3.83641 ( 1164) SS BOND : bond 0.00276 ( 5) SS BOND : angle 1.88264 ( 10) covalent geometry : bond 0.00291 (10776) covalent geometry : angle 1.57487 (14627) *********************** 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: 19 poor density : 75 time to evaluate : 1.326 Fit side-chains REVERT: A 46 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8648 (pp) REVERT: A 118 GLN cc_start: 0.8984 (tt0) cc_final: 0.8751 (tt0) REVERT: A 122 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7340 (tp30) REVERT: A 126 GLN cc_start: 0.8706 (tm-30) cc_final: 0.7995 (tm-30) REVERT: A 244 PHE cc_start: 0.8157 (m-80) cc_final: 0.7568 (m-10) REVERT: A 324 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8857 (tp) REVERT: A 504 LEU cc_start: 0.6466 (tt) cc_final: 0.6223 (tt) REVERT: A 507 MET cc_start: 0.6067 (tpt) cc_final: 0.5659 (tpt) REVERT: A 711 ILE cc_start: 0.8330 (mm) cc_final: 0.8081 (mm) REVERT: B 119 ASP cc_start: 0.8337 (t0) cc_final: 0.7687 (t0) REVERT: B 125 ASP cc_start: 0.8596 (t0) cc_final: 0.8167 (t0) outliers start: 19 outliers final: 15 residues processed: 92 average time/residue: 0.1822 time to fit residues: 26.5687 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 : 1.199 ------------------------------------------------------------------------------- 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 324 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 A residue 730 ILE Chi-restraints excluded: chain A residue 806 THR 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 19 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 116 optimal weight: 0.5980 chunk 35 optimal weight: 20.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.126742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.081539 restraints weight = 18392.595| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.37 r_work: 0.2852 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3286 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= 0.205 Angle : 1.604 34.463 14646 Z= 0.581 Chirality : 0.155 1.889 1659 Planarity : 0.004 0.045 1842 Dihedral : 31.281 179.802 1939 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.72 % Favored : 93.12 % Rotamer: Outliers : 1.61 % Allowed : 16.18 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1294 helix: 1.23 (0.24), residues: 539 sheet: -0.65 (0.42), residues: 147 loop : -1.54 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 12 HIS 0.003 0.001 HIS A 290 PHE 0.020 0.001 PHE A 870 TYR 0.016 0.001 TYR C 21 ARG 0.003 0.000 ARG B 136 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 2) link_NAG-ASN : angle 2.26254 ( 6) link_BETA1-4 : bond 0.00617 ( 1) link_BETA1-4 : angle 0.77349 ( 3) hydrogen bonds : bond 0.04696 ( 412) hydrogen bonds : angle 4.06785 ( 1164) SS BOND : bond 0.00373 ( 5) SS BOND : angle 2.25268 ( 10) covalent geometry : bond 0.00494 (10776) covalent geometry : angle 1.60300 (14627) ********************** 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 89 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 1.196 Fit side-chains REVERT: A 46 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8649 (pp) REVERT: A 118 GLN cc_start: 0.8967 (tt0) cc_final: 0.8758 (tt0) REVERT: A 122 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7381 (tp30) REVERT: A 126 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8017 (tm-30) REVERT: A 244 PHE cc_start: 0.8182 (m-80) cc_final: 0.7576 (m-10) REVERT: A 324 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8800 (tp) REVERT: A 504 LEU cc_start: 0.6479 (tt) cc_final: 0.6244 (tt) REVERT: A 591 MET cc_start: 0.8374 (ptp) cc_final: 0.8132 (ptp) REVERT: A 711 ILE cc_start: 0.8407 (mm) cc_final: 0.8128 (mm) REVERT: A 933 ASP cc_start: 0.9175 (t0) cc_final: 0.8942 (t0) REVERT: B 119 ASP cc_start: 0.8346 (t0) cc_final: 0.7825 (t0) REVERT: B 125 ASP cc_start: 0.8650 (t0) cc_final: 0.8225 (t0) outliers start: 18 outliers final: 15 residues processed: 87 average time/residue: 0.1859 time to fit residues: 26.0774 Evaluate side-chains 89 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 324 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 A residue 730 ILE Chi-restraints excluded: chain A residue 806 THR 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 69 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.129537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.084617 restraints weight = 18354.590| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.40 r_work: 0.2905 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3440 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= 0.110 Angle : 1.569 33.405 14646 Z= 0.560 Chirality : 0.157 1.902 1659 Planarity : 0.004 0.045 1842 Dihedral : 31.222 179.571 1939 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.49 % Favored : 94.44 % Rotamer: Outliers : 1.70 % Allowed : 16.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.24), residues: 1294 helix: 1.55 (0.24), residues: 530 sheet: -0.49 (0.42), residues: 147 loop : -1.41 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 89 HIS 0.001 0.000 HIS A 290 PHE 0.013 0.001 PHE A 538 TYR 0.013 0.001 TYR C 21 ARG 0.003 0.000 ARG B 136 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 2) link_NAG-ASN : angle 1.98541 ( 6) link_BETA1-4 : bond 0.00471 ( 1) link_BETA1-4 : angle 0.83507 ( 3) hydrogen bonds : bond 0.03620 ( 412) hydrogen bonds : angle 3.81372 ( 1164) SS BOND : bond 0.00231 ( 5) SS BOND : angle 1.76883 ( 10) covalent geometry : bond 0.00244 (10776) covalent geometry : angle 1.56880 (14627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7077.21 seconds wall clock time: 121 minutes 58.77 seconds (7318.77 seconds total)